On 9/17/13 8:17 AM, shahab shariati wrote:
Dear Justin
Thanks for your time and consideration.
As I suggested before, visualize the output file and figure out what is
around atom 618 to cause such forces.
I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc
molecule (this dopc molecule is intact and is not broken). There are other
dopc and cholesterol molecules around atom 618. How I understand what
around this atom cause such forces.
Excuse me. Please give me more explanation about your suggestion.
Usually when large forces arise, the cause is fairly obvious. There will be
some atom very close to the one on which the maximum force acts. It may not
always be obvious.
May be, I did not understand your mean truly.
Should I remove this dopc molecule and then run minimization again?
No.
PRODRG generates notoriously bad parameters, particularly the charges.
I know this issue, charges and charges groups obtained from prodrg (in itp
file) were compared with charges and charges groups in similar structures
being in rtp file of gromos (because my drug is very similar to cytosine).
Then I corrected them.
OK, that's a reasonable starting point.
-Justin
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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