[AMBER] gaff+charmm36 in amber vs namd

From: Jio M <jiomm.yahoo.com>
Date: Mon, 12 Dec 2011 04:07:26 -0800 (PST)

Dear ALL,

In brief (but pardon me for long mail) I want to perform simulation of system with GAFF( with RESP charges) parameters and lipid membrane with CHARMM36 ff.

I am still confused even there was discussion regarding usage of gaff + charmm in AMBER engine (e.g. by Dr. Ross Walker   http://archive.ambermd.org/201108/0015.html)

I have following query:

1) Does the compatibility (sorry very rough term) of GAFF molecule with CHARMM36 ff membrane can only be declared after running test simulations and comparing with experimental results and Does scaling of non bonding terms effect this..?

2) I have amber prmtop/inpcrd file for GAFF molecule and amber prmtop/inpcrd for CHARMM36 ff membrane (generated by CHAMBER module).

Now I need to combine both structures to see there interaction, so is there any way to combine two prmtop files and later translation can be done?

I think using getting pdb files for both can help and I can append both structures in xleap. But it needs paramater files. For gaff things are Ok but if I use TOP2FF command for membrane.prmtop I get parameter file not in frcmod format (membrane.prmtop, membrane.frcmod attached) and loadamberparams membrane.frcmod give errors like (Unknown keyword: OSLP -PL - in parameter file and others like this)

3) If I am able to get combined prmtop (gaff+charmm) will sander/pmemd in AMBER11  be able to understand from combined prmtop file which have GAFF and CHARMM to use which code in sander/pmemd, as it was written in amber tool11 manual "The additional code within sander and pmemd to evaluate the extra CHARMM energies and forces." and also "Once a CHARMM prmtop file is produced by chamber, the sander and pmemd dynamics engines automatically detect the presence of CHARMM parameters in the prmtop file and automatically select the correct parameters and code paths ")??

or I should use combined prmtop/inpcrd file in NAMD???
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Received on Mon Dec 12 2011 - 04:30:03 PST
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