AMBER Archive (2004)

Subject: Re: AMBER: Atom distance

From: bybaker_at_itsa.ucsf.edu
Date: Mon Sep 27 2004 - 15:39:49 CDT

('binary' encoding is not supported, stored as-is) Hi,

I try to use ptraj to measure the distance between two atoms. This is my input:

trajin model1-3-md1.crd
distance first out model1-3-md1-dist1.dist 84_at_ND2 197_at_O time 0.1
strip :WAT
go

But it is seems blocked somehow. Please help.

Bo

This is the output:

guanine.6% ptraj model1-3.prmtop < model1-3md1-dist1.in
Read in control variables
Read in atom names...
Read in charges...
Read in masses...
Read in IAC (atoms involved in L-J)...
Read in NUMEX (index to excl atom list)...
Read in NNO (index for nonbond of @type)...
Read in residue labels...
 LEU TYR SER ASP GLN GLU LEU ALA TYR LEU
 ---
 ASN HID LEU ARG LYS ARG LEU GLU
 SER HID PRO ALA WAT WAT WAT WAT WAT WAT
 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
 ...
 WAT WAT WAT
Read in the residue to atom pointer list... 

----
Read in box information...
Successfully completed readParm.

PTRAJ: Processing input file...
       Input is from standard input

PTRAJ: trajin model1-3-md1.crd
Checking coordinates: model1-3-md1.crd

PTRAJ: distance first out model1-3-md1-dist1.dist 84_at_ND2 197_at_O  time 0.1

-----stop at here.

==============Original message text===============
On Mon, 27 Sep 2004 7:12:59 GMT Tomas Linhart wrote:

Try to use ptraj distributed with Amber 7. For me it seems much more
flexile than carnal.

Tomas

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