[gmx-users] renaming DILE to ILE for Charmm27?

[Justin Lemkul]

On 10/23/16 9:35 PM, Mijiddorj Batsaikhan wrote:
> Dear gmx users,
>
> I want to make a simulation the peptide that contains D-ILE using Charmm27
> force field. Is it possible to rename the from DILE to ILE? and use pdb2gmx
> to generate topology of the peptide.
>

There's a lot more to it.  CHARMM supports D-amino acids, but none of those 
parameters are available in GROMACS.  The D-amino acids use a unique CA type 
that then requires distinct bonded parameters, and most importantly, a totally 
different CMAP matrix.  We discussed this in the last week or so; see that 
thread in the archive for more details.

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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