On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
thank you for your answer.
Now I tried it with two different restraint .itp files. One for the
protein and one for the dummy atoms.
But still it doesn't work. Now the error is:
[ file posre_memb.itp, line 5 ]:
Atom index (4942) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
But I think I included it the right way:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "amber03.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber03.ff/ions.itp"
#include "amber03.ff/dum.itp"
#ifdef POSRES
#include "posre_memb.itp"
#endif
In my coordiate file the difference between them look like this:
313LEU HD23 4938 3.813 4.505 3.308
313LEU C 4939 3.435 4.335 3.190
313LEU OC1 4940 3.429 4.330 3.090
313LEU OC2 4941 3.337 4.305 3.259
314DUM DUM 4942 1.996 2.371 6.171
314DUM DUM 4943 1.996 2.371 6.271
314DUM DUM 4944 1.996 2.471 6.171
314DUM DUM 4945 1.996 2.471 6.271
my restraint file for the protein looks like this:
; position restraints for Protein-H of GROup of MAchos and Cynical Suckers
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
4 1 1000 1000 1000
7 1 1000 1000 1000
10 1 1000 1000 1000
13 1 1000 1000 1000
and my restraint file for the dummy atoms look like this:
; position restraints for Protein-H of GROup of MAchos and Cynical Suckers
[ position_restraints ]
; i funct fcx fcy fcz
4942 1 1000 1000 1000
4943 1 1000 1000 1000
4944 1 1000 1000 1000
4945 1 1000 1000 1000
What is wrong?
Atom numbering is done per [moleculetype] and has nothing to do with the atom
numbers in the coordinate file. If you have a one-atom dummy [moleculetype],
then the only valid content of posre_memb.itp is:
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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