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: [email protected] 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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Please don't post (un)subscribe requests to the list. Use the
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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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