AMBER Archive (2009)

Subject: Re: [AMBER] divcon error during antechamber run, convergence problem

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Sat Mar 07 2009 - 09:58:19 CST

I did as you said and I've also deleted END, TER lines in the PDB, now it works correctly.
Thank you!

Best regards,
Andrew

06.03.09, 21:33, "David A. Case" <case_at_biomaps.rutgers.edu>:

> On Fri, Mar 06, 2009, Andrew Voronkov wrote:
> > I've tried to rewrite this PDB file by use of Chimera, DS visualizaer
> > or Gold-Hermes software, but these programms give the same PDB
> > result.
> Your coordinates are not in the correct columns in the pdb file.
> Compare the top few lines in the LIG file:
> ATOM 1 C1 LIG 1 -11.531 -4.269 17.640
> ATOM 2 C2 LIG 1 -12.760 -4.099 18.149
> ATOM 3 C3 LIG 1 -13.317 -5.417 18.529
> ATOM 4 N4 LIG 1 -12.434 -6.371 18.252
> with those in sustiva.pdb (which is correct):
> ATOM 1 C1 SUS 1 0.728 1.403 0.255
> ATOM 2 H1 SUS 1 -0.136 1.756 0.782
> ATOM 3 C2 SUS 1 0.803 0.080 -0.150
> ATOM 4 C3 SUS 1 -0.290 -0.932 0.158
> You will need to have everything in the correct column for your pdb file
> to be properly interpreted. Also, you have dos line endings in the
> "LIG" file--not sure what antechamber might be doing with those.
> ....dac
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-- 
Best regards,
Andrew Voronkov,
PhD student,
Chemistry department, 
Moscow State University

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