AMBER Archive (2008)

Subject: AMBER: problems with ptraj and strip waters

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Sep 18 2008 - 16:19:25 CDT

Thanks for your comments, Carlos

 

I tried on a Window VMD and a Linux VMD and in both cases when I added
the topology file first with"Amber7 parm" followed by the "Amber
Coordinates", I got the same error "....number of atoms could not be
dtermined".

 

This topology file (without water) recognizes the mdcrd when I use
rdparm and reads out how many frames.

 

Also, VMD has no problem reading the topology files and correct states
residues etc.

 

My input file is as follows for making the trajectories without water:

 

trajin file.mdcrd

strip :WAT

 

center :1-2495 mass origin

image origin center familiar

 

trajout file_no_water.mdcrd nobox

 

go

 

 

Steve Seibold

Research Asst. Professor

seibold_at_chemistry.msu.edu

19B Chemistry Building

Michigan State University

East Lansing, MI 48824

Office 517-355-9715 ext 264

 

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