[gmx-users] Setting custom atoms in FF

[Justin Lemkul]

On 3/30/15 10:10 PM, Alex wrote:
> I am not sure if your answer was a resounding "yes".

I don't have the time or desire to build something, test it, and give you an 
absolute answer :)  I can only tell you what the code says, which I can do quickly.

> I am talking about the label on the left in PDB.
>

...which in this case would have to match the entry in the .n2t

> Let us say I want to name my atoms "TEST1" and "TEST2" and set up my
> PDB as
>
> ATOM      1  TEST1   CNT A   1       xxx  yyy   zzz  1.00  0.00
> ATOM      2  TEST2   CNT A   1       xxx  yyy   zzz  1.00  0.00
>
> and then in atomname2type.a2t I put
>
> TEST1   opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
> TEST2   opls_1001   0.1    12.011  3    C  0.142  C 0.142  C 0.149
>
> will the resulting topology contain the distinction despite the issue with bond
> lengths? If not, what would be the correct syntax to do that?
>

This should work (sorry, again I can't be "resounding" in my answer).

> I just want to define my atoms in a way that supplements (actually,
> precedes) what x2top does when the atoms are not specifically labeled.
> A tedious solution in my case, but definitely viable, if this works.
>

Make a toy system.  Three C atoms in a line, the bond length between one of them 
at 0.149 and the other at 0.142, terminal carbons with different names, and an 
.n2t entry with two lines, specifying these connections.  That will tell you if 
you're on to something or not.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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