On 7/20/13 7:35 AM, afsaneh maleki wrote:
Dear users
To generate a topology file for an arbitrary molecule, I used g_x2top
program.
I added following lines to atomname2type.n2t:
..
..
C opls_145B 0.080627 12.0110 3 C 0.1395 C 0.1395 C 0.149
C opls_145B 0.091698 12.0110 3 C 0.149 C 0.1395 C 0.1395
You're going to have problems. Both of these lines specify the same criteria to
assign different charges to a given atom.
..
But, generated topology file is as the following:
.
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
..
..
17 opls_145 1 TPT C15 1 0.037549 12.011 ;
qtot -0.4087
18 opls_145 1 TPT C12 1 0.037549 12.011 ;
qtot -0.3712
..
I don’t know, why g_x2top program replaces opls_145B (in .n2t) with
opls_145 atom type to generate topology file?
Apparently the opls_145B criteria (distances to neighboring atoms) are not
satisfied, but the opls_145 criteria are.
-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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