From: Gan, Yong \(UMC-Student\) (yg8p2_at_mizzou.edu)
Date: Thu Apr 28 2005 - 11:58:02 CDT
Thank you for your kind replies!
The pdb file I downloded is for GROMACS. However, before I change atom names in the pdb file, I need to know the corresponding relation of atom names between the pdb file and top_all27_prot_lipid.inp. For example, in the pdb file, the first atom ia named "CA". So, what is the atom name of "CA" in the file "top_all27_prot_lipid.inp"?
From: Marcela P. Aliste [mailto:marcela.aliste_at_biology.gatech.edu]
Sent: Thu 4/28/2005 10:56 AM
To: Gan, Yong (UMC-Student)
Subject: Re: namd-l: Generate psf file of DMPC membrane
I did it for POPC, I modify the names of the PDB file or you can use alias pdb
name to changed, also you have to rename the residue becuase gromacs use DMP and
you have to use DMPC.
I am not sure that the atoms int eh PDB nedd to have the same order that
> I download a DMPC pdb file at "www.ucalgary.ca/~tieleman/download.html" and
> tried to generate the psf file using VMD. But, it doesn't work. I think it's
> because the atom names in the pdb file are not same as those in
> "top_all27_prot_lipid.inp". Who has done this before? Could you tell me how
> to solve it?
-- Dr. Marcela P. Aliste Postdoctoral Fellow School of Biology Georgia Tech 310 Ferst Dr. Atlanta, GA 30332-0230 Phone: (404) 385-4714 Fax: (404) 894-0519
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