[gmx-users] DMPC bilayr

[Anton Feenstra]

> Itamar Kass wrote:
> 
>    Dear fellows, I am trying to use some of the files taken from Dr. Tieleman
> homepage without any successful.  I downloaded the files lipid.itp and copied
> the entries under atomtypes and nonbond_params to the relevant sections in
> ffgmxnb.itp.  I also download dmpc.itp in order to use the almN4start.pdb
> structure (in which I think there is DMPC bilayr).
>    I entered my pepteid using InsightII V.98 creating the file merged.pdb and
> used "editconf -f merged.pdb -o start.gro" to create a .gro file in which I
> changed all the POP molecules into DMPC molecules.  Then I used "pdb2gmx -f
> start.gro -p merged.top -o merged.gro -ignh" (with the OPLS-AA/L all-atom force
> field) to produced the files neede. The program responded was "Atom C in residue
> DMSO 1 not found in rtp database".
>    Does someone know how to solve it?  Thanks you for your help, Kass.


First, if you modify ffgmxnb.itp, and then select OPLS in pdb2gmx,
you will *not* use the Gromacs forcefield, and *not* use your 
modified parameters in ffgmxnb.itp.

Second, the problem is DMSO is not in the OPLS forcefield.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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