From: mustapha.hamdi_at_ensi-bourges.fr
Date: Fri Feb 09 2007 - 18:41:51 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,
>> >
>> >
>
Dear Lea and Cesar,
Thanks for your help! Now I can do aliases with the correct atoms names.
Bon Weekend !
Mustapha
-- Mustapha Hamdi PhD student Laboratoire Vision et Robotique ENSI de Bourges 10 Bd Lahitolle 18000 Bourges France. Tel: (+33) 2 48 48 40 59 WebSite: http://perso.ensi-bourges.fr/hamdi/
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