[AMBER] problem with new residu in Xleap

From: Muriel Jourdan <Muriel.Jourdan.univ-grenoble-alpes.fr>
Date: Tue, 17 May 2016 16:15:10 +0200

Hi,

I have troubles with new defined residu in Xleap. I have defined
a new DPRO (D-proline) called CPR residu in Xleap with new frcmod,
prmtop and library file....
and set head and tail info as follow

head .R< CPR 1> . A < N 1>
tail .R < CPR 1 > .A < C 13>

and did the same for a modified fluorescein called ff (new library,
frcmod....)

head .R < ff 1 > .A < NZ 47>
tail .R < ff 1 > .A <015 25 >

I have then constructed in Xleap a peptide using the following command:

peptide = sequence { ACE ALA ARG ....... GLY DPRO .......GLY ff}
and the peptide looked very fine when I edited it in xleap.
I was also able to save the prmtop and incprd file (see the attached
file) but with error message:

"Making per-residu atom chain type"
(residues lacking connect 0/connect 1 - these don't have chain type marked)
DPRO
ff

When I looked at the details for DPRO (desc DPRO.1 and desc ff.1) the
line connection atoms is empty.

My problem is that even a simple minimization does not work. Sander is
running but does not generate any .out and .rst
files. Can anyone help me?
Many thanks in advance

Muriel


-- 
Muriel JOURDAN
D├ępartement de Chimie Mol├ęculaire
Batiment Nanobio
570 rue de la Chimie
BP 53 38041 GRENOBLE Cedex 9
Tel : (+00 33) (0)4 56 52 08 39
nouvelle adresse : muriel.jourdan.univ-grenoble-alpes.fr




_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber




Received on Tue May 17 2016 - 07:30:04 PDT
Custom Search