[gmx-users] Adding a residue

[Justin A. Lemkul]

Smith, Chanel Chonda wrote:
> Could anyone give me the proper procedure for adding a residue?  (Using itp)
> 

http://oldwiki.gromacs.org/index.php/Tutorials#General

See the drug-enzyme tutorial, but be advised that PRODRG topologies often 
contain unsatisfactory charges and charge groups, requiring manual modification 
and validation (as with any method of deriving parameters, really).

-Justin

> ________________________________
> 
> From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
> Sent: Thu 8/13/2009 1:51 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Adding a residue
> 
> 
> 
> 
> 
> Smith, Chanel Chonda wrote:
>> Hello,
>>     I am currently using GROMACS 4.  When trying to process the pdb file
>> with pdb2gmx, an error message came up stating that a particular residue
> was
>> not recognized by the residue topology database.  I then tried to adding a
>> molecule in the ff....rtp file and adding the name in aminoacids.dat.  This
>> did not work either.  The residue that I need to add is a nonprotein.
> Could
>> you tell me how I can add this residue to the database and therefore
> allowing
>> me to process the pdb file?
>>
> 
> You've followed the correct procedure.  If the new residue is a ligand of
> some
> sort, it may just be easier to create an .itp file for it (using one of the
> user-contributed programs, or something like PRODRG).
> 
> If you still want to use the .rtp approach, provide more details, like the
> actual .rtp entry and the exact error message that you're getting from
> pdb2gmx.
> 
> -Justin
> 
>> Thanks,
>> Chanel King
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> 
> --
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================