[gmx-users] Atomtype OW not found - spc water model

[Justin Lemkul]

On 4/8/14, 11:18 AM, Carlos Navarrro Retamal wrote:
> Hello everyone,
> I'm trying to perform a MD of a mixture of solvent (in my case glycerol+water).
> In order to do that i first obtained the parameters of glycerol on CHARMM on here -> par_all36_carb.prm. To use this parameters on gromacs i used the psf2topol.py script ->https://github.com/resal81/PyTopol, generating a .top and a .itp file respectively.
> Just to try these files, i create a box with 2 molecules of glycerol and add 106 water molecules (SPC)-> Gly_solv.gro file.
> Finally, when i edit the topol.top file i add the next line: #include "charmm27.ff/spc.itp", to include the parameters of the SPC water model, but when i run grommp to make a minimization of the system i got the next error message:
>
>> Fatal error:
>> Atomtype OW not found
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
> but if i remove the water (and of course the include line into the topol.top file) grommp works just fine :/
> I really don't know what may be happening.

In theory, the CHARMM27 files that come with Gromacs can support SPC, but in 
practice, there is no reason for you to do it.  CHARMM force fields are 
parametrized for use with TIP3P; other water models risk invalidating the force 
field.

-Justin

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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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