[gmx-users] Minimizing a molecule not recognised by gromacs

Justin Lemkul jalemkul at vt.edu
Thu Jul 19 14:30:33 CEST 2007

> Hi All,
> My molecule of concern is not recognised by gromacs3.3. I have added
> the following to the ffoplsaa.atp file:
> CR51       13.01900  ; aromatic CH-group (5-ring), united [SS]
>  CR61       13.01900  ; aromatic CH-group (6-ring), united
>  NR5*       14.00670  ; aromatic N (5-ring, 3 bonds)
>  CB         12.01100  ; bare carbon (5-, 6-ring)
>  OM         15.9994   ; =0 connected to aromatic (6-ring)
> data is obtained from the PROGRD web-based software.

I have only done a little bit of work with small molecules, so take my advice
for what it's worth.  I doubt you need to modify any .atp files to get this to
work.  I don't know about PROGRD, but with PRODRG, you can download a topology
file of your small molecule.  Include this molecule.itp file in your system
topol.top and you should be fine.  Note that PRODRG is only useful with
GROMOS87 and GROMOS96 force fields (the beta version provides for both).

> But the software is not working properly after that. It was OK after
> the lines added was removed.
> Can anyone help me in this matter, if there is anything more to be
> done, or to be done the other way?
> Subhrangshu Supakar
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Justin A. Lemkul
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu
(540) 231-9080


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