Dear all,
I generated topology of a ligand (ATP) using Acpype which gave me the topology file topol.top and conf3_GMX.itp. I'm writing a report and confused as to what I should write in the report, "I'm using GAFF force field for ATP" or "OPLS/AA force field for ATP". The top line of the topol.top file says #include "oplsaa.ff/forcefield.itp" which caused the confusion. Although the conf3_GMX.itp file seems to have everything and I don't think Gromacs is taking any parameters from "oplsaa.ff/forcefield.itp" file but still I want to be sure. I have attached the topol.top and conf3_GMX.itp file.
My system has only ligand (ATP) and water.
Thanks and Regards,
Raghav
Hi Raghav
ACPYPE generate the topology and parameter file for the small molecules with force fields like AMBER99SB or GAFF. The topologies generated according to the format of GROMACS (_GMX.itp, _GMX.top, _GMX.gro), OPLS (_GMX_OPLS.itp and same), CNS (_CNS.top and same). Thus without breaking the compatibility of the force field, the topologies generated can be used in AMBER force field or OPLS force field as ported in the GROMACS.
In your case, you have selected the itp file of the GROMACS format and top file of the OPLS format.
Dear Anu Manhas
Thanks but the question is still unanswered, my system has only ligand and water
So that means the OPLS focefield parameters are not being used at all since the _GMX.itp file has everything? Am I right?
Regards,
Raghav
Dear Raghav
Your .top file contain a syntax
; Include forcefield parameters #include "oplsaa.ff/forcefield.itp"
Which reflects that you want to add the OPLS force field parameters but in reality, you have not selected the OPLS parameter file. So, it will not read at all.
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