I have just found the problem right now:
set DPRO.1 connect0 DPRO.1.N
set DPRO.1 connect1 DPRO.1.C
and the same for the ff residu (set the connect0 and connect 1 the same
as head and tail
respectively) and it works now.
Muriel
e 17/05/2016 16:15, Muriel Jourdan a écrit :
> 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
>
>
>
>
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--
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 - 08:30:03 PDT
