[gmx-users] error in residue topology

[Justin A. Lemkul]

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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-- 
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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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