Bhawana Gupta wrote:
Dear gmx-users,
i made earlier asked this question .but there is a problem.
first i got the error:
-------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: futil.c, line: 527
Fatal error:
Library file posre.itp not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
Then on your advice, i put posre.itp in my directory, but i again got an
error.
-------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 1196
Fatal error:
[ file posre.itp, line 9 ]:
Atom index (5) in position_restraints out of bounds (1-3).
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.
-------------------------------------------------------
Interestingly, this exact question was asked just a few days ago:
http://www.gromacs.org/pipermail/gmx-users/2008-November/037675.html
It would serve you well to search the archives; many answers can be found there.
And furthermore, grompp is giving you advice about how to solve the problem.
Something in your .top is out of order.
<snip>
then i again make a posre.itp file , which i like this
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
[ position_restraints ]
; atom type fx fy fz
AFTER THAT I GOT NO ERROR.
TELL ME WHETHER I AM CORRECT AT THIS POINT.
Well, then you're applying no position restraints, which I suppose is not what
you are after.
-Justin
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--
========================================
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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