[gmx-users] Question about topology construction.
jalemkul at vt.edu
Thu Mar 20 17:54:12 CET 2014
On 3/20/14, 10:21 AM, sujithkakkat . wrote:
> I am using gromacs-4.6.5. For the sake of practice, I made a .itp file
> for carbon dioxide based on the EMP2 model (J.Phys.Chem 1995, 99,
> 12021-12024) .
> The file is self-contained with all parameters including the [default]
> and [atomtypes].
> I tried to do run a simulation on a system containing only CO2 molecules.
> My topology file included only the .itp which I made and no other
> forcefield.itp is included. (Is it ok to do so?)
> When I try to generate .tpr for an energy minimization, I get the error
> "Found a second defaults directive" which the manual says is due to second
> defaults being set in an included topology file.
> BUT, Here I am defining 'default' only once, which is in the .itp file
> for CO2 which I made and no other .itp from any forcefield is included. So
> I am not sure how it is the "second" default and what is causing the
> error. Is it necessary that the .itp should be included in some forcefield
> directory although it has all the parameters, and then include it into .top
> as a subset of the forcefield?
> Please let me know what you think.
> Have a look at the .itp I made for CO2 and please let me know if anything
> is seriously wrong.
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 3 no 1.0 1.0
> ; name mass charge ptype sigma epsilon
> CA 12.01100 0.6512 A 0.2757 0.2339
> CO 15.99940 -0.3256 A 0.3033 0.6695
> ; name nrexcl
> CO2 1
> ; nr type resnr residue atom cgnr charge mass
> 1 CA 1 CO2 CA 1 0.6512 12.0110
> 2 OC 1 CO2 OC1 1 -0.3256 15.9994
> 3 OC 1 CO2 OC2 1 -0.3256 15.9994
> ; i j funct doc
> 1 2 1 0.1149
> 1 3 1 0.1149
> 1 2 3
> 2 1 3
> 3 1 2
> ; i j k funct a0 ak
> 1 2 3 1 180 1236
Linear angles may not be stable, just a forewarning. I think some improvements
have been made to the code over the years to help fix previous issues.
This #endif doesn't match any #ifdef above.
Your .itp file is almost an entire .top, anyway, but if there is an issue, it's
probably coming from the .top level.
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
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