From: Lea Thøgersen (lea_at_daimi.au.dk)
Date: Fri Feb 09 2007 - 16:33:01 CST
Hi Mustapha,
if you source the attached list of aliases, it should do the trick.
Regards
Lea
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of Cesar Luis Avila
> Sent: 9. februar 2007 19:37
> To: mustapha.hamdi_at_ensi-bourges.fr
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: DMPC psf.
>
> Dear Mustapha,
> as you should know, gromacs uses a united atom representation for
> hydrogens, ie, hydrogen atoms are implicitly modeled. That's why you see
> the difference in the number of atoms. Moreover, each forcefield has
> it's own nomenclature for the atoms in the molecule, so you would have
> to use aliases in psfgen in order to use that pdb. After that, the
> missing hydrogens can be guessed.
> I used to have a script to transform that exact file into charmm's
> topology/coordinate files. As soon as I find it I will send it to you
> (ok, IF i find it).
> Regards
> Cesar
>
>
> mustapha.hamdi_at_ensi-bourges.fr escribió:
> > Dear all,
> >
> > I'm trying to generate the DMPC membrane psf file using
> > http://www.ucalgary.ca/~tieleman/files/dmpc_npat.pdb . I founded that
> the
> > DMPC residue Charmm27 and Gromacs are not the same, the Gromacs DMPC
> > residue have 46 atoms and Charmm top_all27_lipid one have 118 atoms. Is
> > there a way to generate DMPC psf file ?
> > PS: the attached: DMPC.pdb and DMPC gromacs topology file.
> >
> > Best regards,
> >
> >
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