questions about "psfgen".

From: Lv Shouqin (
Date: Sat Jun 12 2004 - 00:12:14 CDT

Dear ALL,
I have a question about ¡°psfgen¡±. Following the user¡¯s guide of NAMD,
the ¡°psfgen¡± can get the XPLOR format of ¡°psf¡± file, but I compared the
difference between the psf file generated by ¡°psfgen¡± of NAMD and that
generated by XPLOR, and found that their differences lie in two aspects:
The first is that the former format file lack of the correct description of
¡°DONOR¡± and ¡°ACCEPTOR¡± of HBONDS, so I can not do HBOND analysis
correctly by the program XPLOR using this psf file;
The other is that the former format file can not give right description of
¡°cutoff¡± algorithm, i.e. the NGRP is always 1. So the speed of the energy
analysis is very slow.
Maybe you will say that these problems can be solved through generating psf
file by XPLOR but not ¡°psfgen¡± of NAMD, but the difficulty is that there
are not corresponding XPLOR format of CHARMM force field files which were
used in NAMD, and I did not know how to change the format easily if not by
So, I want to know: Can and how to get all consistent psf file of XPLOR
format by the ¡°psfgen¡± of NAMD, i.e. correctly description of ¡°DONOR¡±
and ¡°ACCEPTOR¡± of HBOND and included ¡°CUTOFF¡± design? Thanks a lot!
Shouqin Lv

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