quasih again

From: <dkon_at_email.arizona.edu>
Date: Tue 18 Dec 2001 12:30:05 -0700

Thank you to David Case for answering my last query. However, quasih
seems to have a limit on the number of atoms which is not mentioned
in the documentation. When I try to run it with the following command:
$AMBERHOME/exe/quasih -nat 1471 -f 2 -m mass -x np4.xyz.13.str -v np4.13.vecs
-first 1 -last 308 -lastvec 20 < np4.tr.13.str
It gives me the following error:
Too many atoms specified: 1471 240
This is apparently independent of both the trajectory file and of
the mass input file - so quasih can only handle up to 240 atoms?
That seems incredible. I would appreciate your help! Thank you,

From rajaamber6_at_rediffmail.com 19 Dec 2001 09:15:56 -0000
Message-id: <20011219091556.9351.qmail.mailweb34.rediffmail.com>
Date: 19 Dec 2001 09:15:56 -0000
From: Raja Swaminathan <rajaamber6_at_rediffmail.com>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: diffusion
In-Reply-to: <sc19c344.>

Dear amber users

1. I have done a 2ns MD on DNA duplex and i want to analyse water and counterions over the entire run.

2. what is the exact physical meaning of diffusion and correlation option in ptraj. what it does exactly.

Please provide me some example inputs regarding the queries.

Thanking you in advance

Raja Swaminathan
Received on Tue Dec 18 2001 - 11:30:05 PST
Custom Search