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
Département de Chimie Moléculaire
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
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Received on Tue May 17 2016 - 07:30:04 PDT
