RE: minimization problem

From: Ahmet Bakan (abakan_at_ku.edu.tr)
Date: Thu Mar 18 2004 - 18:43:00 CST

Hi Again,

CT2 C CT3 exactly means that you have a wrong atom type for an atom in your
topology file, because C is for alpha carbon of amino acids. You should use
this atom type for backbone alpha carbon atoms, since there is no such
parameter. If you guess that parameter, you will have the same trouble with
torsional parameters. You should check your atom type definitions.
Sorry for sending two emails.

Ahmet

==========ABC==========
Ahmet Bakan
Chemistry, Junior
Koc University
abakan_at_ku.edu.tr
ICQ #86167698
http://home.ku.edu.tr/~abakan
 

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Olya Kravchenko
Sent: Friday, March 19, 2004 1:32 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: minimization problem

Dear all! I have the following problem:

I'm trying to minimize the structure of part of the molecule that I have
edited by myself into the topology file (heme A type) and thus edit
parameter
file for missing bonds and angles (measure them in vmd, then write those
into
the parameter file with constants from similar bonds and angles that are
already in parameter file). I get the following error:

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 C CT3
Aborted

But I don't have such an angle in my structure! The atom types that I
assigned
to my structure seem to be correct. What can I do to resolve this?

Thank you very much in advance!

Olya

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