[gmx-users] Increase the box size or decrease rlist

[Justin Lemkul]

On 8/20/14, 12:56 PM, pragna lakshmi wrote:
> Thank you Mark for ur reply.
> In the generated POPC.top from POPC.pdb and POPC.psf using VMD, the charges
> have become to zero. Here are few lines of my POPC.top
>
> [ atomtypes ]
> ; name bond_type mass charge ptype sigma epsilon
> C1 C 1.0 0.0 A 0.0 0.0
> C11 C 1.0 0.0 A 0.0 0.0
> C12 C 1.0 0.0 A 0.0 0.0
> C13 C 1.0 0.0 A 0.0 0.0
>
> [ atoms ]
> ; nr  type  resnr residue atom cgnr charge  mass
>       1           N      1     POPC      N      1     0.0000    14.0070
>       2         C11      1     POPC    C11      2     0.0000    12.0110
>       3         C12      1     POPC    C12      2     0.0000    12.0110
>       4         C13      1     POPC    C13      3     0.0000    12.0110
>
> My question is whether this could be the reason for not having the charges
> over the atoms.
> If it is so, could you please suggest me the proper way of getting
> parameters for POPC (charmm36 ff).
>

The proper parameters are published and are included in the .rtp file for 
CHARMM36 that our lab produced.  There is no reason to run anything through VMD; 
it looks like it produces a shell of a topology that is totally nonfunctional.

-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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