[gmx-users] how to create a PEO Residue database

[Justin A. Lemkul]

lammps lammps wrote:
> Hi everyone,
>  
> The structural formula of PEO is CH3-- O- CH2 - CH2 - (O - -CH2 - CH2 )n 
> - O - -CH2 - CH2 - O - CH3
>  
> I have obtain all the OPLS-AA FF for PEO from a paper such as  
> atomtypes,  bondtypes, angletypes, and dihedraltypes. Then I have a .PDB 
> of PEO.  I need a residuce to create .top and .gro.
>  
> The questions are
>  
> 1. What is the suitable residuce datebase of PEO I must create 
> myselt for the command pdb2gmx conversing PDB to .top and .gro?
>  

Read the manual for the appropriate format.  In addition, this link might 
provide some general guidance:

http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html

> 2. If there is a suitable residuce,  what file should I change except 
> the ffoplsaa.rtp?
>  

Perhaps the .hdb, if you are missing any hydrogen atoms.

-Justin

> Any suggestion is appreciated. Thanks in advance.
> 
> -- 
> wende
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

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