Chanchal wrote:
Hi Justin,
Thanks for the info. I know that the topologies are provided in that
website. But they have used charmm27 ff and converted it to gromacs format.
But I want to use gromos96 45a3 ff.
Does that force field support sugar/membrane interactions? Can it model
sugars separately, and membranes separately? Is there evidence the
combination might also work?
I have another question. Suppose I use those topologies for dopc . And for
the sugar part, I use gromos96 45a3. Will it create problem when we combine
sugar /dopc system?
Yes. See http://oldwiki.gromacs.org/index.php/Force_Fields
Mark
Thanks
Chanchal
On Tue, Aug 18, 2009 at 7:46 PM, Justin A. Lemkul <[email protected]> wrote:
Chanchal wrote:
Hi All,
I am a novice in gromacs. I want to study sugar/membrane interaction and
I want to use gromos96 45a3 ff. At first I am planning to simulate dopc
bilayer + water. I downloaded the pdb file of dopc from the site
http://www.bioinf.uni-sb.de/RB/ . Then I typed pdb2gmx_d -f dopc.pdb and
choose gromos96 45a3 force field. But I got the error "Residue 'OLE' not
found in residue topology database". How can I fix the error?
This happens because pdb2gmx is not magic. See here:
http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
The website you reference provides suitable topologies for this type of
simulation, making pdb2gmx unnecessary.
-Justin
Thanks
Chanchal
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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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