[gmx-users] regarding DOPC lipid parameters

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Apr 21 13:40:43 CEST 2007

Hi Nagaraju,

You're mail is rather inaccessible in regards the language. Please try
to phrase your question in clear english, which will be of benefit to
you, as it makes it easier for people to read and answer your

I believe you're problem relates to the parameterization of a lipid
which is not yet available. I'm not sure what force field you want to
use, but the best way to tackle this (and the most didactical) is to
draw DPPC and/or POPC and indicate all atom names, numbers, types and
charges, bonds, pairs, angles, dihedrals and improper dihedrals. Then,
draw your DOPC and do the same, taking the same types for
corresponding atoms, bonds, angles, etc. After that, write the
topology, taking one of the available ones as a template.



On 4/21/07, naga raju <nagaraju_cy at yahoo.co.in> wrote:
> Dear Gromacs Users,
>                               I searched mailing list for DOPC lipid bilayer
> paramters. I found in one of the mailing list "For CHARMM parameters (which
> I believe Feller uses), there is POPC in top_all27_prot_lipid.rtf. For the
> united atom lternative,
> Tieleman's website has popc.itp. In either case, just copy it to a new DOPC
> definition and modify the palmitoyl into another oleoyl"
>     I looked into DPPC.itp and POPC.itp files, it very confused (bonds,
> angles and dihedrals) to me to prepare DOPC.itp.  Can any body tell how to
> combined these file and getting DOPC parameters.
>            any suggestion is appriciated,
>                             Thanks in advance,
>              With regards,
>             Nagaraju Mulpuri.
>  ________________________________
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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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