ADL: read in atom charge

xiaoqin huang xqhuang1018 at msn.com
Tue Mar 18 08:26:34 PDT 2008


hi, dockers,
anyone knows how to make the autogrid4 or autodock4 read the atomic charge in the format of F7.4(8.4) instead of F6.3?
because the atomic charges derived from amber or ab initio calculations are usually in F7.4. after read in autodock, it takes format F6.3, so the partial charge and total charge are not the exact as the original ones.
 
xiaoqin
 
03/18/2008
 
 
> From: autodock-request at scripps.edu> Subject: autodock Digest, Vol 48, Issue 27> To: autodock at scripps.edu> Date: Mon, 17 Mar 2008 10:47:10 -0700> > Send autodock mailing list submissions to> autodock at scripps.edu> > To subscribe or unsubscribe via the World Wide Web, visit> http://mgldev.scripps.edu/mailman/listinfo/autodock> or, via email, send a message with subject or body 'help' to> autodock-request at scripps.edu> > You can reach the person managing the list at> autodock-owner at scripps.edu> > When replying, please edit your Subject line so it is more specific> than "Re: Contents of autodock digest..."> > > Today's Topics:> > 1. Update.. (Antonio Cavazzuti)> 2. better linux release (Antonio Cavazzuti)> 3. Re: better linux release ( Gon?alo Justino )> 4. Continue a docking ? (Nikolaos Mitakidis)> 5. Re: Continue a docking ? (Cyril Bauvais)> 6. Parameters (Giulia Canevari)> 7. Re: Update.. (Sargis Dallakyan)> 8. Docking inside recptor (David Crosby) (Antonio Cavazzuti)> 9. small molecule-small molecule docking (surasak chunsrivirot)> > > ----------------------------------------------------------------------> > Message: 1> Date: Mon, 17 Mar 2008 10:47:17 +0100> From: "Antonio Cavazzuti" <acavazzuti at ipb.csic.es>> Subject: ADL: Update..> To: autodock at scripps.edu> Message-ID: <20080317093943.M8911 at ipb.csic.es>> Content-Type: text/plain; charset=iso-8859-1> > Hi, > I run ADT1.5 on Ubuntu 7.1. > This morning I tried to update ADT and I got this answer from python shell:> > > > > Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07) > [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2> Type "copyright", "credits" or "license()" for more information.> > ****************************************************************> Personal firewall software may warn about the connection IDLE> makes to its subprocess using this computer's internal loopback> interface. This connection is not visible on any external> interface and no data is sent to or received from the Internet.> ****************************************************************> > IDLE 1.2.1 ==== No Subprocess ====> >>> Exception in Tkinter callback> Traceback (most recent call last):> File "/home/antonio/MGLTools-1.5.0/lib/python2.5/lib-tk/Tkinter.py", line> 1403, in __call__> return self.func(*args)> File "/home/antonio/MGLTools-1.5.0/MGLToolsPckgs/Support/update.py", line> 598, in updateTested> self.getUpdates()> File "/home/antonio/MGLTools-1.5.0/MGLToolsPckgs/Support/update.py", line> 171, in getUpdates> self.clearUpdates()> File "/home/antonio/MGLTools-1.5.0/MGLToolsPckgs/Support/update.py", line> 631, in clearUpdates> os.rmdir(update_dir)> OSError: [Errno 2] No such file or directory:> '/home/antonio/MGLTools-1.5.0/MGLToolsPckgs/Updates/tested'> > Is this a problem? If so, how can I fix it?> Thanks,> Antonio> > > > > ------------------------------> > Message: 2> Date: Mon, 17 Mar 2008 10:58:30 +0100> From: "Antonio Cavazzuti" <acavazzuti at ipb.csic.es>> Subject: ADL: better linux release> To: autodock at scripps.edu> Message-ID: <20080317095605.M14139 at ipb.csic.es>> Content-Type: text/plain; charset=iso-8859-1> > Hi,> Is there a suggested LINUX RELEASE for Autodock4 suite installation?> Thanks,> Antonio> > > ------------------------------> > Message: 3> Date: Mon, 17 Mar 2008 10:19:02 +0000> From: " Gon?alo Justino " <goncalo.justino at gmail.com>> Subject: Re: ADL: better linux release> To: autodock at scripps.edu> Message-ID:> <f6f8c1a80803170319u6001aee3j8eed7d19300106ff at mail.gmail.com>> Content-Type: text/plain; charset=ISO-8859-1> > well, the install runs perfectly on the latest fedora distros (7 and 8, from> dvd) and autodock (& ADT) runs just fine. no extra libraries needed!> > Gon?alo> > On 17/03/2008, Antonio Cavazzuti <acavazzuti at ipb.csic.es> wrote:> >> > Hi,> > Is there a suggested LINUX RELEASE for Autodock4 suite installation?> > Thanks,> > Antonio> > ________________________________________________> > --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---> >> > > ------------------------------> > Message: 4> Date: Mon, 17 Mar 2008 04:12:56 -0700 (PDT)> From: Nikolaos Mitakidis <nmitakidis2 at yahoo.com>> Subject: ADL: Continue a docking ?> To: autodock at scripps.edu> Message-ID: <65053.95697.qm at web62201.mail.re1.yahoo.com>> Content-Type: text/plain; charset=us-ascii> > Dear all,> > while performing a flex docking of 250 runs, a hardware power down occurred and my job was stopped at run 190.> Does anyone know any way to continue the docking from that point, and continue writing output to the same .dlg file? > > I was wondering whether any additional flags are used from autodock4 (apart from -l), for such an occasion.> > Thank you a lot in advance.> Nikos> > > > > > > > ____________________________________________________________________________________> Looking for last minute shopping deals? > Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping> > ------------------------------> > Message: 5> Date: Mon, 17 Mar 2008 12:45:13 +0100> From: Cyril Bauvais <cyril.bauvais at u-psud.fr>> Subject: Re: ADL: Continue a docking ?> To: autodock at scripps.edu> Message-ID: <47DE59C9.50608 at u-psud.fr>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed> > Runs are independant with autodock so you can run another job of 60 jobs > and read them two, using autodocktools.> > Cyril Bauvais> > > > > --> > > > > > ------------------------------> > Message: 6> Date: Mon, 17 Mar 2008 16:43:14 +0100> From: "Giulia Canevari" <giulia.canevari at gmail.com>> Subject: ADL: Parameters> To: ADL <autodock at scripps.edu>> Message-ID:> <c1dab2a50803170843p154a8d72o5fec0676f0cd388a at mail.gmail.com>> Content-Type: text/plain; charset=ISO-8859-1> > Hi Autodockers,> > I have a (maybe stupid, but I would like to know) question the default> parameters used by Autodock to model the interactions between atoms:> where are they taken from (or how are they obtained)?> > Thanks in advance,> > Giulia> > # $Id: AD4_parameters.dat,v 1.14 2007/04/27 06:01:47 garrett Exp $> #> # AutoDock> #> # Copyright (C) 1989-2007, Garrett M. Morris, David S. Goodsell, Ruth> Huey, Arthur J. Olson,> # All Rights Reserved.> #> # AutoDock is a Trade Mark of The Scripps Research Institute.> #> # This program is free software; you can redistribute it and/or> # modify it under the terms of the GNU General Public License> # as published by the Free Software Foundation; either version 2> # of the License, or (at your option) any later version.> #> # This program is distributed in the hope that it will be useful,> # but WITHOUT ANY WARRANTY; without even the implied warranty of> # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the> # GNU General Public License for more details.> #> # You should have received a copy of the GNU General Public License> # along with this program; if not, write to the Free Software> # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA> 02110-1301, USA.> > # AutoDock Linear Free Energy Model Coefficients and Energetic Parameters> # Version 1.0> # $Revision: 1.14 $> > # AutoDock 4 free energy coefficients with respect to original (AD2)> energetic parameters> #> # Free Energy Coefficient> # ------> FE_coeff_vdW 0.1560> FE_coeff_hbond 0.0974> FE_coeff_estat 0.1465> FE_coeff_desolv 0.1159> FE_coeff_tors 0.2744> > # AutoDock 4 Energy Parameters> > # - Atomic solvation volumes and parameters> # - Unweighted vdW and Unweighted H-bond Well Depths> #> # - Atom Types> # - Rii = sum of vdW radii of two like atoms (in Angstrom)> # - epsii = vdW well depth (in Kcal/mol)> # - vol = atomic solvation volume (in Angstrom^3)> # - solpar = atomic solvation parameter> # - Rij_hb = H-bond radius of the heteroatom in contact with a> hydrogen (in Angstrom)> # - epsij_hb = well depth of H-bond (in Kcal/mol)> # - hbond = integer indicating type of H-bonding atom (0=no H-bond)> # - rec_index = initialised to -1, but later on holds count of how> many of this atom type are in receptor> # - map_index = initialised to -1, but later on holds the index of the> AutoGrid map> # - bond_index = used in AutoDock to detect bonds; see "mdist.h", enum> {C,N,O,H,XX,P,S}> #> # - To obtain the Rij value for non H-bonding atoms, calculate the> # arithmetic mean of the Rii values for the two atom types.> # Rij = (Rii + Rjj) / 2> #> # - To obtain the epsij value for non H-bonding atoms, calculate the> # geometric mean of the epsii values for the two atom types.> # epsij = sqrt( epsii * epsjj )> #> # - Note that the Rij_hb value is non-zero for heteroatoms only, and> zero for H atoms;> # to obtain the length of an H-bond, look up Rij_hb for the> heteroatom only;> # this is combined with the Rii value for H in the receptor, in AutoGrid.> # For example, the Rij_hb for OA-HD H-bonds will be (1.9 + 1.0)> Angstrom,> # and the weighted epsij_hb will be 5.0 kcal/mol * FE_coeff_hbond.> #> # Atom Rii Rij_hb rec_index> # Type epsii solpar epsij_hb map_index> # vol hbond bond_index> # -- ---- ----- ------- -------- --- --- - -- -- --> atom_par H 2.00 0.020 0.0000 0.00051 0.0 0.0 0 -1 -1 3> # Non H-bonding Hydrogen> atom_par HD 2.00 0.020 0.0000 0.00051 0.0 0.0 2 -1 -1 3> # Donor 1 H-bond Hydrogen> atom_par HS 2.00 0.020 0.0000 0.00051 0.0 0.0 1 -1 -1 3> # Donor S Spherical Hydrogen> atom_par C 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0> # Non H-bonding Aliphatic Carbon> atom_par A 4.00 0.150 33.5103 -0.00052 0.0 0.0 0 -1 -1 0> # Non H-bonding Aromatic Carbon> atom_par N 3.50 0.160 22.4493 -0.00162 0.0 0.0 0 -1 -1 1> # Non H-bonding Nitrogen> atom_par NA 3.50 0.160 22.4493 -0.00162 1.9 5.0 4 -1 -1 1> # Acceptor 1 H-bond Nitrogen> atom_par NS 3.50 0.160 22.4493 -0.00162 1.9 5.0 3 -1 -1 1> # Acceptor S Spherical Nitrogen> atom_par OA 3.20 0.200 17.1573 -0.00251 1.9 5.0 5 -1 -1 2> # Acceptor 2 H-bonds Oxygen> atom_par OS 3.20 0.200 17.1573 -0.00251 1.9 5.0 3 -1 -1 2> # Acceptor S Spherical Oxygen> atom_par F 3.09 0.080 15.4480 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Fluorine> atom_par Mg 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Magnesium> atom_par MG 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Magnesium> atom_par P 4.20 0.200 38.7924 -0.00110 0.0 0.0 0 -1 -1 5> # Non H-bonding Phosphorus> atom_par SA 4.00 0.200 33.5103 -0.00214 2.5 1.0 5 -1 -1 6> # Acceptor 2 H-bonds Sulphur> atom_par S 4.00 0.200 33.5103 -0.00214 0.0 0.0 0 -1 -1 6> # Non H-bonding Sulphur> atom_par Cl 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Chlorine> atom_par CL 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Chlorine> atom_par Ca 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Calcium> atom_par CA 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Calcium> atom_par Mn 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Manganese> atom_par MN 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Manganese> atom_par Fe 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Iron> atom_par FE 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Iron> atom_par Zn 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Zinc> atom_par ZN 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Zinc> atom_par Br 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Bromine> atom_par BR 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Bromine> atom_par I 4.72 0.550 55.0585 -0.00110 0.0 0.0 0 -1 -1 4> # Non H-bonding Iodine> > > ------------------------------> > Message: 7> Date: Mon, 17 Mar 2008 09:45:32 -0800> From: Sargis Dallakyan <sargis at scripps.edu>> Subject: Re: ADL: Update..> To: autodock at scripps.edu> Message-ID: <47DEAE3C.1050300 at scripps.edu>> Content-Type: text/plain; charset=us-ascii; format=flowed> > Antonio Cavazzuti wrote:> > Hi, > > I run ADT1.5 on Ubuntu 7.1. > > This morning I tried to update ADT and I got this answer from python shell:> > > > > > > > > > Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07) > > [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2> > Type "copyright", "credits" or "license()" for more information.> > > > ****************************************************************> > Personal firewall software may warn about the connection IDLE> > makes to its subprocess using this computer's internal loopback> > interface. This connection is not visible on any external> > interface and no data is sent to or received from the Internet.> > ****************************************************************> > > > IDLE 1.2.1 ==== No Subprocess ====> > > >>>>Exception in Tkinter callback> > > > Traceback (most recent call last):> > File "/home/antonio/MGLTools-1.5.0/lib/python2.5/lib-tk/Tkinter.py", line> > 1403, in __call__> > return self.func(*args)> > File "/home/antonio/MGLTools-1.5.0/MGLToolsPckgs/Support/update.py", line> > 598, in updateTested> > self.getUpdates()> > File "/home/antonio/MGLTools-1.5.0/MGLToolsPckgs/Support/update.py", line> > 171, in getUpdates> > self.clearUpdates()> > File "/home/antonio/MGLTools-1.5.0/MGLToolsPckgs/Support/update.py", line> > 631, in clearUpdates> > os.rmdir(update_dir)> > OSError: [Errno 2] No such file or directory:> > '/home/antonio/MGLTools-1.5.0/MGLToolsPckgs/Updates/tested'> > > > Is this a problem? If so, how can I fix it?> > Hi Antonio,> > I've done a couple of changes in Support/update.py to make it more robust. Grab > one of our nightly builds and replace your .../MGLToolsPckgs/Updates with the > one included in the tarball or do CVS update.> http://mgltools.scripps.edu/downloads/nightly> > Thanks,> Sargis> http://mgltools.scripps.edu/blog> > > ------------------------------> > Message: 8> Date: Mon, 17 Mar 2008 17:51:40 +0100> From: "Antonio Cavazzuti" <acavazzuti at ipb.csic.es>> Subject: ADL: Docking inside recptor (David Crosby)> To: autodock at scripps.edu> Message-ID: <20080317164504.M91071 at ipb.csic.es>> Content-Type: text/plain; charset=iso-8859-1> > Hi David, > did you solved the problem concerning the docking inside the receptor?> (problem reported in autodock Digest, Vol 48, Issue 17)> If yes, can you suggest me how to avoid this problem?> Thank you!> Antonio> > > > > > 1) I've noticed often when I attempt to dock a ligand I'll get > > a handful (perhaps 5 in 25-50) of dockings where the ligand is > > docked quite literally inside the macromolecule resulting in some > > astronomical dG value. Is there some setting I'm missing when I set > > up my grids or docking parameters to tell Autodock to avoid > > nonsensical dockings? I see you can specify an upper energy limit > > under the docking parameters menu, but can I assign a lower limit to > > avoid these wild results? They throw off the clustering data. I'm > > attempting to dock a somewhat small molecule with 4-6 torsions onto > > a relatively small receptor (~6kd,) I'm trying to keep my initial > > dockings unbiased, so my grid envelops the entire receptor. I've > > left plenty of space for the ligand to rotate freely in all > > configurations, so why does my ligand often end up inside my > > receptor instead of on the surface? I understand autodock first > > introduce 50 randomly placed/oriented ligands inside the grid volume > > and make calculations from there, but why would it consider > > molecules making obviously high-energy (or low) contacts with other > > atoms as preferable dockings?> > > > > ------------------------------> > Message: 9> Date: Mon, 17 Mar 2008 17:47:07 +0000> From: surasak chunsrivirot <fa833 at hotmail.com>> Subject: ADL: small molecule-small molecule docking> To: <autodock at scripps.edu>> Message-ID: <BLU134-W2745170B9C28196C74453AF0050 at phx.gbl>> Content-Type: text/plain; charset="iso-8859-1"> > > Hi,> > I am new to docking software and currently trying to find a software that can dock and calculate binding energy of small molecule-small molecule such as a drug molecule and solvent. Can Autodock do this kind of calculation? I've look at the website and it said it can do small molecule-protein and protein-protein docking.> > If it can't do this, I would appreciate if you have any suggestions for a software that I should use.> > Thank you very much,> Surasak> > > > > > _________________________________________________________________> Helping your favorite cause is as easy as instant messaging.?You IM, we give.> http://im.live.com/Messenger/IM/Home/?source=text_hotmail_join> > ------------------------------> > ________________________________________________> --- ADL: AutoDock List --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---> > End of autodock Digest, Vol 48, Issue 27> ****************************************
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