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

[Justin Lemkul]

On 5/26/14, 2:20 PM, shivangi nangia 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.
>

Providing us with the actual error message is vastly more helpful.

> 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.
>

If you need to use a different force field, you need to generate a new topology 
under that force field.  CHARMM36 is superior to other versions of the force 
field, especially for lipids, so take that into consideration.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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