VMD-L Mailing List

From: dipti lele (diptisl86_at_gmail.com)
Date: Tue Oct 21 2008 - 08:42:18 CDT

Hello All,

   I am new to VMD. I am using psfgen to geenrate a psf file for the
membrane which I have generated by membrane plugin of VMD. Although I have
received the file psf file along with it I am not able to regenerate it
manually. when I make a segment called "LIP" from the pdb file without
water. It gives error like "reading residues from pdb file myfile_prot.pdb
duplicate residue key 1
ERROR: failed on residue POPE from pdb file
duplicate residue key 2
ERROR: failed on residue POPE from pdb file
duplicate residue key 3......."

When I scanned the file then I found that there are 2 POPE molecules which
have residue number 2. But they have been created by VMD.

One more error : no atom C in residue POPE:1 of segment U
Warning: add conformation failed in patch NTER

Should I do patching?

I am not able to find out the error. And at the end psf file contains less
no of atoms so I cant use them for NAMD.

Is it that I am missing some step?

Thanking you.

With Regards 

-- 
Deepti Lele,
NII, New Delhi.