[gmx-users] Regarding DOPC parameters

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 1 15:48:11 CEST 2007

Hi Nagaraju,
> 1)      I would like to use 43a1 force field to my protein (transmembrane
> protein). May I combine this force field with dopc.itp.

a. Check the page you got the lipid parameters from for a reference.
b. If the lipid parameters are not for 43a1 you can't just mix them
with a 43a1 defined protein

> 2)      Mr. Chris Neale said that modification of C6 and C12 parameters to
> sigma, epsilon when merging lipid.itp and OPLSAA. Corresponding link was
> given below.
> http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html

a. If that was what he said, he didn't finish his sentence :)
b. If the lipid parameters are not for OPLSAA you can't just mix them
with a OPLSAA defined protein

> 3)      If I have to modify lipid.itp file, I request you that can you give
> more details about modification of parameters and file format.

a. For the modification of parameters, check the papers about the
force field you want to define the parameters for.
b. For the file format, read the manual chapter 5 (and look at the
various .itp files in the gromacs data directory).
>                             Any suggestion is appreciated. Thank you in
> advance.

You're welcome :)



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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