[gmx-users] ligand

‪farial tavakoli‬ ‪ farial.tavakoli at ymail.com
Mon Aug 14 08:04:01 CEST 2017

Dear Justin
Thanks for your advice.Now I am trying to create a .gro file from the united atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o xxx.gro
but faced to this warning:
WARNING: all CONECT records are ignored
would you please advice me how can i solve this problem?
thanks alotFarial

      From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org 
 Sent: Sunday, 13 August 2017, 21:45:53
 Subject: Re: [gmx-users] ligand

On 8/13/17 12:29 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear justin
> Thank you for your replyI thought that topology file obtained from ATB needs to be changed like PRODRG

No, they generally should not.  ATB is a much better topology source than 
PRODRG.  That doesn't necessarily mean you should always trust a black box 
without some validation, but you shouldn't just blindly go messing with things 
because some other program is known to be problematic.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129

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