Re: PSF generation

Date: Sun Dec 07 2003 - 19:12:58 CST

Please note that PDB files are column based, and everything must appear in the
correct column(s). In other words, it's not safe to add or remove spaces between
data in a PDB file. You can compare your file to a standard PDB file (e.g., one
downloaded from the Protein Data Bank), and make sure that every field (especially
the resid field) be in the same columns in both files.
Ying Xiong

>Subject: namd-l: PSF generation
>Hi all,
>I have defined a residue of 127 atoms for a polymeric chain sample. PDB file for
one residue ends as below:
>ATOM 121 H37A PEU 1 10.644 13.121 4.7ATOM 122 H37B PEU 1
  10.636 11.621 3.7ATOM 123 H35A PEU 1 8.672 12.464 5.9ATOM
124 H35B PEU 1 8.331 12.205 4.2ATOM 125 HN7 PEU 1 10.782
 12.241 7.5ATOM 126 HN8A PEU 1 14.809 13.096 7.1ATOM 127 HN8B
PEU 1 14.063 12.139 5.8The problem is that NAMD psfgen finds no
residue. When I shift residue_name column to one left, psfgen finds a residue but
does not read last 40 atoms. Is column with restricted in PDB files?? How can I
overcome this problemThank you very much,Ahme
> ==============ABC==============
>Ahmet BAKAN
>Chemistry, JunioKoc #8616769

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:13 CST