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Nuno Azoia wrote:
Hi Justin. Tank you for your answer!
Ok! I agree with you, and I'm doing something wrong. I just can
understand what. Can you please help me a little more.
In my .top file I have this lines
-----------------------------------------------------------
; Include chain topologies
#include "krt_spd_C.itp"
#include "krt_spd_A.itp"
#include "krt_spd_B.itp
-----------------------------------------------------------
That should be fine.
The krt_spd_C.itp is the topology of a peptide with 244 atoms.
krt_spd_A.itp and krt_spd_B.itp are peptides with 435 and 418 atoms,
respectively. In the last line of each .itp file I have something like
this (the letter changes with the corresponding file name)
-----------------------------------------------------------
; Include Position restraint file
#ifdef POSRES
#include "posre_A.itp"
#endif
-----------------------------------------------------------
This might be the problem. You're calling an .itp file from within an .itp
file. That may work, but I've never tried it. Each .itp file should provide
the parameters for a single molecule, no more. What I would try is the following:
; Include chain topologies
#include "krt_spd_C.itp"
#ifdef POSRES_C
#include "posre_C.itp"
#endif
#include "krt_spd_A.itp"
#ifdef POSRES_A
#include "posre_A.itp"
#endif
#include "krt_spd_B.itp"
#ifdef POSRES_B
#include "posre_B.itp"
#endif
That way, each chain topology is followed by its corresponding position
restraint file, under the appropriate [ molecule ] definition.
-Justin
Each posre_*.itp file has positions restraints for all the atoms in the
peptide. For instance, posre_A.itp is something like this:
-----------------------------------------------------------
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
(...)
430 1 1000 1000 1000
433 1 1000 1000 1000
434 1 1000 1000 1000
435 1 1000 1000 1000
------------------------------------------------------------
Ok. In version 3.3.1 that's all I used to do. But now version 4.0
demands a posre.itp file, an so I've created this one, and at least by
this way grompp are reading my files
------------------------------------------------------------
; Include posre topology
#include "posre_A.itp"
#include "posre_B.itp"
#include "posre_C.itp"
------------------------------------------------------------
That's why I can not understand what I'm doing wrong.
Another thing that I'm finding surprising is that, with two different
systems, in two different simulations, I get the same error in the 15th
position.
Thank you for your time.
Nuno Azoia
On Tue, 2008-11-04 at 13:14 -0500, Justin A. Lemkul wrote:
Quoting Nuno Azoia <[EMAIL PROTECTED]>:
Hi!
I'm having problems with grompp in version 4.0.
When I attempt to run grompp I get this message. I've tried with two
different systems, but the message is exactly the same
-------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 1196
Fatal error:
[ file posre_A.itp, line 16 ]:
Atom index (15) in position_restraints out of bounds (1-14).
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.
-------------------------------------------------------
I'm not understanding why is "Atom index (15)" out of bounds. The range
(1-14), where did it came from?
grompp is finding a 15th atom to which it is trying to apply position
restraints, but it is unable to.
It seems that I just can only have 14 position_restaints conditions, but
this don't make any sense to me. Can anyone help with this? What do I
have to do to solve this problem?
The error message is pretty clear - you have inserted #include "posre.itp"
within the incorrect molecule definition (i.e., it is in the wrong order or
wrong section in the .top).
-Justin
Tank you
Nuno Azoia
--
Nuno Gonçalo Azoia Lopes
Laboratório de Investigação em Acabamento
Departamento de Engenharia Textil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal
Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293
Mobile: +351 965 382 487
E-mail: [EMAIL PROTECTED]
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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