[gmx-users] Adding a residue
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 14 18:29:49 CEST 2009
Smith, Chanel Chonda wrote:
> Could anyone give me the proper procedure for adding a residue? (Using itp)
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).
> 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:
>> 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
>> 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.
>> you tell me how I can add this residue to the database and therefore
>> me to process the pdb file?
> You've followed the correct procedure. If the new residue is a ligand of
> 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
>> Chanel King
>> gmx-users mailing list gmx-users at gromacs.org
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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