[gmx-users] defining impropers necessary?

Justin Lemkul jalemkul at vt.edu
Wed Jul 17 16:48:14 CEST 2013

On 7/17/13 10:37 AM, gromacs query wrote:
> Dear All,
> I have some polymer having peptide bond and want to use OPLSaa. I was
> following Justin's example for building polymers
> http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html
> I have few queries:
> 1) do I need to define improper for peptide in .rtp file to keep it planar?

If the parent force field uses these terms, yes.

> 2) Also can pdb2gmx write improper by itself (in out .top file) depending
> upon bond information and atom types defined in rtp file? Then there will
> be no need to define impropers in rtp

There's an easy way to find out :)  Otherwise, if you know what you want, 
specify it and be 100% certain.

> 3) Also can I use + before atom name more than once in one residue
> (fragmented polymer)

My gut says yes, but a real example would be helpful.  You can certainly use the 
+ indicator on multiple lines and (I think) even within the same line.



Justin A. Lemkul, Ph.D.
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


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