[gmx-users] Setting custom atoms in FF

[Justin Lemkul]

On 3/29/15 4:07 PM, Alex wrote:
> Hi all,
>
> I am messing with the OPLS/AA forcefield. The idea is to functionalize
> graphene edge atoms beyond passivation with hydrogen. At the
> functionalization region, there is a C atom with
> two C-C bonds (from graphene), while the third bond is formed with the
> functional group. The particular atom from the functional group
> intended to bond with that C bond is also carbon. When setting up the system, in atomname2type.n2t I have:
>
> CJ   opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142  ; bulk graphene C
>
> but also want to introduce
>
> CJ   opls_1001   0.1    12.011  3    C  0.142  C 0.142  C 0.149  ; edge C
>
> Both 996 and 1001 are defined in the ffnononbonded.itp, these are
> custom, but essentially copies from oplsaa entries for carbon. Note
> the third bond that's longer (which is also the case in my input PDB).  The
> significant difference is of course the charge there, as I want a globally neutral
> system.
>
> Here is the problem: x2top ignores the second statement from above and the
> functionalized edge C is assigned #996. Aside from manually modifying
> the resulting topology, can we make this distinction stick?
>

g_x2top (and other programs like pdb2gmx) use a default ± 10% distance tolerance 
for deciding if something is within bonding distance.  The distinction between 
0.149 and 0.142 is about 5%, so the two lines are effectively indistinguishable. 
  The most straightforward solution would be to change the default tolerance in 
the code, if your distances are going to be so close in magnitude.

-Justin

-- 
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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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