[gmx-users] Backward (CG to atomistic), no charmm27

Tsjerk Wassenaar tsjerkw at gmail.com
Mon May 26 20:54:05 CEST 2014

Hi sxn,

That's a bit odd. Possibly the version of the CHARMM POPC mapping on
cgmartini.nl does not have charmm27 under the [ mapping ], but it should be
added then. There is no difference in terms of backmapping. Anyway, you can
use the charmm36 like you did. It will use your force field settings as
dictated by the atomistic topology. There is nothing specific for charmm36
versus charmm27 in backward or initram.



On Mon, May 26, 2014 at 8:20 PM, shivangi nangia
<shivangi.nangia at gmail.com>wrote:

> Hello,
> I was able to convert my coarse grained system to all-atom using the
> backward script.
> However, it (Mapping folder) only had option for charmm36.
> I have an all-atom .gro file and .top file for charmm36 but I need t run my
> simulations with charmm27.
> Doing pdb2gmx with all-tom .gro file runs into error which I believe is for
> mismatch in atom types between charmm36 and 27.
> Also,on using the command (./initram.sh -f system.gro -f system_aa.top -po
> backmapped.top -from martini -to charmm27)  handled the protein part of the
> system but ran into error for POPC, but changing -from martini -to charmm36
>  successfully converted to all atom.
> Please suggest.
> Thanks,
> sxn
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Tsjerk A. Wassenaar, Ph.D.

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