Hi Dan
Yes. Rdparm reads through correctly, stating the number of sets in the trajectory. RMSD and distances can be also calculated without a problem.
Thanks Steve
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Monday, February 21, 2011 3:00 PM
To: AMBER Mailing List
Subject: Re: [AMBER] PTRAJ and segmentation faults
Hi,
Is ptraj able to read through the trajectory at all? Does the segfault
occur without the 'contacts' command?
-Dan
On Mon, Feb 21, 2011 at 3:56 PM, Seibold, Stephen <Seibold79.stmary.edu> wrote:
> Hi users
> I am having problems with the latest ToolSet version. I tried running "contacts" in ptraj and keep getting a "segmentation fault". I am sending you my input file and log file.
>
> Am I doing something wrong? I also tried using a PDB as input instead of .mdcrd, but it also gave me the segmentation fault.
>
> INPUT:
>
> trajin RNAP_openMD39_42.mdcrd
>
> center :1-2495 mass origin
> image origin center familiar
>
> contacts first byresidue out contact.txt time 10 distance 5.0 .CD
>
>
> go
>
>
> OUTPUT LOG FILE:
>
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 11.0 integrated" (4/2010)
> -/- Executable is: "ptraj"
> /-\ Running on 1 processor(s)
> \-/ Residue labels:
>
> MET GLU ILE LYS ARG PHE GLY ARG ILE ARG
> GLU VAL ILE PRO LEU PRO PRO LEU THR GLU
> ILE GLN VAL GLU SER TYR ARG ARG ALA LEU
> GLN ALA ASP VAL PRO PRO GLU LYS ARG GLU
> ASN VAL GLY ILE GLN ALA ALA PHE ARG GLU
> THR PHE PRO ILE GLU GLU GLU ASP LYS GLY
> LYS GLY GLY LEU VAL LEU ASP PHE LEU GLU
> TYR ARG LEU GLY GLU PRO PRO PHE PRO GLN
> ............
> ............
>
> WAT WAT WAT WAT WAT WAT WAT
>
> PRMTOP does not contain %FLAG RADIUS_SET
> Setting box to be an exact truncated octahedron, angle is 109.471221
>
> PTRAJ: Processing input from "STDIN" ...
>
> PTRAJ: trajin RNAP_openMD39_42.mdcrd
> Checking coordinates: RNAP_openMD39_42.mdcrd
> ./ptraj: line 1: 5109 Segmentation fault ptraj RNAP_open.prmtop
>
>
>
> I applied all the new patches, recompiled (gcc on Red Hat enterprise 5) and the ToolSet passed all its test. Even with the patches does ptraj have trouble with large trajectories?? I have since switched over to "netCDF" hoping this will stop the problem.
>
> Steve Seibold, Ph.D.
> Assistant Professor of Chemistry
> University of Saint Mary
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Feb 21 2011 - 13:30:06 PST
