AMBER Archive (2004)

Subject: RE: AMBER: ptraj

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue May 25 2004 - 12:35:39 CDT

Dear Holly,
 
You don't say specifically what program you are using to read in your
topology file and also what version of amber you are using. The topology
file you attached is read fine by rdparm in amber 8. Can you read other
topology files ok?
 
I have converted this file to an Amber6 topology file for you using
new2oldparm. Try this version of the parmtop file and see if you still get
an error.
 
If you do then can you please provide us with some more information.
 
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 |

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Holly Freedman
Sent: 25 May 2004 09:17
To: amber_at_scripps.edu
Subject: AMBER: ptraj

Hi,

I am running ptraj on a trajectory generated for CH3Cl in water and am
getting an error when trying to read the prmtop file, which I am attaching.
The error says

Read in info for bonds w/out hydrogen...

ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN

Does anyone know how to get around this bug?
Thanks in advance for your help. If anyone knows how to modify this prmtop
so that ptraj will read it, this would be so helpful to me.

--Holly Freedman
    University of Utah


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu