[gmx-users] The solvation free energy of a vdw ligand

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 17 19:38:49 CET 2012

Tanping Li wrote:
> Hey Justin,
> Thanks for the help. I've generated big size of data so I hope I can find the way to fix the problem before transfer to the new version.
> I just find that it gives me problem when I use the self-defined atom type in the state B, however works fine if I use the existing atom type in the state B.
> I defined the atom types by the following way:
> [ atometypes ]
> ;name      mass     charge  Ptype  C6  C12
> dum_CH3    15.035     0       A     0   0
> ....
> ....
> Did I missed some there? I noticed that the "at. num" is included in the ffgmxnb.itp file. I searched the manual, but haven't find that.

It's the atomic number.  Different force fields have their lines parsed 
differently, unfortunately, so you have to adhere to the existing format.  Add a 
zero in the column for atom number and see if this improves the situation.  I 
would recommend not using ffgmx for anything, though.  The newer manual gives 
several reasons why it's a bad choice for just about any modern simulation.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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