[gmx-users] ligand

[‪farial tavakoli‬ ‪]

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

-- 
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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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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