[gmx-users] PEG residue

[Justin Lemkul]

On 3/17/14, 7:05 PM, dan42 wrote:
> I am new to GROMACS. I am trying to use pdb2gmx to create a topology for PEG
> (O-C-C)n with only H on one terminal and OH on the other. I know that I need
> to add a residue entry to the forcefield for example to aminoacids.rtp in

Well, multiple residues actually, to account for terminal and repeating block 
residues.

http://www.gromacs.org/Documentation/How-tos/Polymers

> the gromos54a7.ff folder. However, I do not know how to construct the
> residue entry. I do know the format but I do not know what values to enter
> for bonds, angles, dihedrals ect. Can anyone help me?

Parameters for alkanes are pretty much cut-and-paste from any residue that has 
CH2-CH2 linkages, in addition to the CH2-O-H groups at the ends.  You can take 
the gb_*, ga_*, and gd_* parameters that you need based on what you find in 
ffbonded.itp - parameters are described in some detail there.

The problem you will have is the ether linkages.  AFAIK there are no parameters 
for ethers in 54A7, though other related force field parameter sets (i.e., those 
for sugars) will have them.  The Gromos parameter sets are all closely linked, 
so the parametrization protocol should yield reasonably compatible parameters. 
It's something you will want to check thoroughly.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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