ADL: non-integral charge error

Mezei, Mihaly mihaly.mezei at mssm.edu
Tue May 12 10:28:19 PDT 2020


Hello, 

Just to see that the total charge is integral number does not exclude non-integral residue charges say, 0.9 on on one and 1.1 on an other. You can use my program Simulaid (http://inka.mssm.edu/~mezei/simulaid) to check for non-integral residue charges. Note that this usually happens if the crystal structure has missing atoms in those residues - those are listed in the PDB file.

Best regards,

Mihaly Mezei

Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai
Voice:  (212) 659-5475   Fax: (212) 849-2456
WWW (MSSM home): http://icahn.mssm.edu/profiles/mihaly-mezei
WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
WWW (Department): http://www.mssm.edu/departments-and-institutes/pharmacology-and-systems-therapeutics


________________________________________
From: autodock-bounces at scripps.edu <autodock-bounces at scripps.edu> on behalf of Sirish R Narayanan <srnaraya at ucsd.edu>
Sent: Tuesday, May 12, 2020 12:09 PM
To: autodock at scripps.edu
Subject: ADL: non-integral charge error

USE CAUTION: External Message.

Hello,

I get a non-integral charge error after preparing my proteins with autodocktools, even though the check total charge says there are no residues with non-integral charges. Why does this error happen, and should I use a different program to assign protein charges? Also I sent this email a week ago and no one responded.

Best,
Sirish Narayanan

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