from CHARM36 to Amber file format

[Riccardo Ocello]

Dear Users and developers,

I'm newer in this community so please apologise me if I'll doing some mistake!
I experienced some problems in file format compatibility with.
What I'll trying to do, are free energy correction using Quantomm on a channel protein (to be precise, correction in the filtration process of K+ ions through the selectivity filter of my protein).

I build my system up and performed MD simulations using NAMD2.12 and/or GROMACS2016 and for both sets of runs, I used CHARMM36 force field.
To be consistent to my original setup, I would continue to use the same ff (I don't want to switch to Amberff), but going through to Sire's tutorials (Quantomm, ligandswap) I noted that I have to use Amber like top and crd.
I tried to convert my PSF using Chamber (included in Parmed, Ambertools2014/2016), but the prmtop which I get appear to be quite different from the real Amber.prmtop topology (they are substantially different in file format, values of charges, and so on).

I searched online if there were some Charm36ff files (prm, rtf, str) good for tleap (in order to create again my topology using consistent parameter), but neither in Mackerrel lab web site nor anywhere else something useful was found.

Does anyone experienced the same problem?
Have you any tips to breaking through this problem?

Thanks in advance for your time!

Cheers,

Riccardo

[Christopher Woods]

  Dear Riccardo,

I am afraid that quantomm currently only supports the Amber forcefields, and is not yet able to read in and use the extra information required for charmm in the chamber-generated topology file. Lester (who you may have met) has written a new charmm forcefield parser and we are working on adding in charmm forcefield support. However this code is not yet ready for use and is not sufficiently tested to allow production running.

Your options are to either wait for us to complete and test the charmm code (likely to be at least another month) or to reparameterise your system using Amber. Reparameterising using Amber would allow you to learn how to use quantomm, and will also add in extra data points to check the sensitivity of the phenomenon you are modelling to the forcefield (i.e. what you observe should be consistent from both amber and charmm forcefields, and it will be interesting to see how the correction free energies differ between different QM models and amber and charmm).

  Best wishes,

  Christopher

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Christopher Woods
+44 (0) 7786 264562
http://chryswoods.com