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 - 05:30:03 PDT
