[gmx-users] How to modify H atom type from opls_369 to match H expected by popc.itp

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 31 13:00:28 CEST 2008

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> Hi all,
> Two days back I posted this question, no one replied thats why I am posting
> again.

It is typically advisable to not post the same question multiple times until you
get an answer.  Try to solve your issue on your own and report back with what
you have done to help yourself.  That said, see pointers below.

> I wanted to use OPLS-AA/L force field for POPC and Protein
> 1.I calculated  the sigma and epsilon values as the way Mr.Justin mentioned
> , the values I got are
>  ;name   name   charge     mass   charge   ptype    sigma           epsilon
>   LO      LO         1        15.9994   0.000      A    0.295999914
> 0.878694594 ;carbonyl O, OPLS
>   LOM   LOM      1        15.9994   0.000      A     0.295999914
> 0.878694594 ;carboxyl O, OPLS
>   LNL    LNL        1        14.0067   0.000     A     3.35300e-03
> 3.95100e-06 ;Nitrogen, OPLS
> 2. Then in first step of Chris procedure(web link quoted below), wrote that
> add atom type H from opls_369 to match H expected by pope.itp
> http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html
> In archives H atom type adding problem posted for pope type of lipids
>   opls_369   H    1   1.008  0.400     A     0.0000e+00   0.0000e+00 (for
> pope)
>  Im using POPC type of lipid
>  I want to ask two things
> 1.  How can I  modify H atom type in popc.itp file

Add an atomtype named H with the same parameters as opls_369.

> 2. Mr. Chris mentioned that Parameters require a double pairs section,  how
> can I mention?

It is quite explicit from point 2 (c) in the post you quote.  Copy the
[pairtypes] section directly from lipid.itp into ffoplsaanb.itp


> Pls give me detail explanation, Eagerly  waiting for reply
> all comments will be appreciated
> Thanks in advance


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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