Hello,
It is question related to gromacs and you will find probably the response in the gromacs manual.
A good start is to compare a set of parameters (for example C -CA) available in parm99.dat file (available in the AnberTools distrib) and the same parameters already converted in the amber99sb.ff force field available the latest distrib of GROMACS. From these files, the conversion will be simple.
HTH
Stephane
________________________________________
De : Anna MARABOTTI [amarabotti.unisa.it]
Date d'envoi : lundi 25 mars 2013 13:12
À : amber.ambermd.org
Objet : [AMBER] problems in parameters calculated with AMBER
Dear Amber users,
I am new to this list, and I am not currently
using Amber. I'd need an help to understand a problem that I have with
Antechamber suite.
I want to calculate parameters for a cofactor of a
green fluorescent proteins, using Amber99SB ff, in order to implement
these parameters into the ff used by GROMACS. I used Antechamber to
perform calculations, following the Antechamber tutorial. I obtained the
.mol2, .frcmod, .prmtop and .inpcrd files regularly.
To implement
these parameters into the Amber99sb forcefield, I have to convert them
since the units are not equal: in the .frcmod I understand that, e.g.
the bond force constant is expressed in kcal/(mol A^2), whereas in the
parameters set in the AMBER99SB forcefield for GROMACS, the force
constant is expressed in KJ/(mol nm^2). Therefore, roughly to convert my
Amber parameters into Gromacs parameters, I should multiply them by
approx. 418.4.
I checked the parameters present in both files, and I
see that the difference is not approx. 400, but approx. 800. I don't
understand what is the source of this factor of 2. I obviously asked the
same to GROMACS users, but I'm checking also with you. Are parameters in
.frcmod file referred only to one atom, or to both (so I have to
multiply - or divide - by 2)?
Could you please give me some hints
about?
Many thanks and best regards
Anna
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Received on Mon Mar 25 2013 - 06:00:06 PDT
