ADL: fragmental volume and solvation parameters

ANURAG BAGARIA anurag.bagaria at gmail.com
Thu Oct 11 05:21:48 PDT 2007


With reference to a previous post (more than 3 years back) at :
http://mgldev.scripps.edu/cgi-bin/perlfect/search/search.pl?q=solvation%20parameter&showurl=%2Fautodock%2F2004-May%2F000105.html

Dear Autodockers,



Is there any web server or stand alone software (Free of cost)

available for the converstion of PDB formated macromolecule to PDBQ
formated one reliably ?

if no such softwares, please give me the formula or methodology to
calculate these atomic

solvation parameter , so I can manually calculate and edit in my PDBQS
file.I am asking this question due to the following problem I
faced....

1)I tried BABEL program to convert PDB(macromolecule) into mol2, then
into pdbq using 'mol2topdbq' program, then added atomic solvation
arameter by 'addsol' parameter but the resulted pdbqs file contains
value of '0' in all fields of coluim number 71 to 76 .What's going
wrong here?

2) I still attempted to use that pdbqs file for further docking study
and got somehow favaourable result...I am wondering now, whether the
positiveresult that I got purely by fluke....otherwise it is the power
of autodock to perform correct docking without atomic solvation
parameter..!

3) Earlier, while using autogrid,the program itself enabled the -o
flag in grid calculation due to the average value of 0 found at 71 to
76 col of the PDBQS file, Please correct me if I am wrong at anywhere
in the format converstion methodology....I don't have commercial
softwares such as InsightII,SYBYL..at this moment etc...

Yours truly,

B.Nataraj



B.Nataraj,
Final year M.Tech.(Bioinformatics),
SASTRA Deemed University,
(www.sastra.edu)
Thanjavur,
Tamil Nadu,
India.
Email:nataraj at biotech2.sastra.edu
<http://mgldev.scripps.edu/mailman/listinfo/autodock>
Email:natarajmtech at yahoo.co.uk
<http://mgldev.scripps.edu/mailman/listinfo/autodock>


I would like to inform that I too did face a similar problem and finally
ended up editing the q.kollua file so as to include some more residue types
(in a different protonation stage) by referring to the Xleap program and
reading about the protonation stages of different residues. But now when
coming to the solvation parameters file I am unable to find the
corresponding values and am stuck up at this point.

Can someone please provide me with some information with regard to residues
ASH and GLH (neutral ASP and GLU respectively). I would be very thankful to
the concerned person.
-- 



ANURAG KUMAR BAGARIA


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