[gmx-users] atomtypes in .n2t

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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