AMBER Archive (2004)

Subject: RE: AMBER: about running ptraj in amber8

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 26 2004 - 11:22:36 CDT

> I was trying to run ptraj in Amber8. But it has problem to read Charmm
> format file (topology psf file). I am wondering if there is any defaut
> Amber format setting? I tried it on the old ptraj version
> (seperated from
> Amber), it worked. Any idea why this happened?

Can you post your psf file please. There is no obvious difference between
amber8 ptraj.c and amber7 ptraj.c that involves the decision on whether a
file is an Amber or Charmm topology file. The code that decides is:

  if (strcmp(buffer, "PSF \n") == 0)
    state = loadCharmmPSF(fp, 1);
  else {
    safe_freopen(fp);

So quickly check the first line of your charmm topology file and see if
contains the string "PSF ".

If you can post me the psf file I can look deeper.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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