mohit kumar wrote:
still im getting problem, i checked the funct its have numerical
value..stilll getting problem..do i have to install gromac 3 version for
that..coz i having 4.0.5 version...
Working with the most recent version (4.0.5) is always recommended. The only
reason to use an old version would be for consistency with older work. Can you
post your [ pairs ] section so we can have a look? What type of machine are you
using? If it's Windows, then there may be problems with the file if it was
edited using anything other than a plain text editor, in which case dos2unix is
your friend.
-Justin
On Thu, Aug 6, 2009 at 3:22 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
mohit kumar wrote:
but i dnt find any 'type' column in my topology file..the grompp
programm with this top file works gud in 3.3 version..im having
4.0.5 version..is that can be issue?? shud i try in 3.3 version
This may be some new error-checking mechanism introduced in version
4.0. In your topology, a function type for pairs should be defined,
according to the header of this section (from pdb2gmx):
[ pairs ]
; ai aj funct c0 c1 c2
c3
If your "funct" column is blank or says "0" then that could be
giving the error.
-Justin
On Thu, Aug 6, 2009 at 2:48 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
mohit kumar wrote:
im running energy minimization for POPC bilayer but its
showing
error which i cant figure out
-- -------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: topdirs.c, line: 99
Fatal error:
Invalid pairs type 0
what does this pair type mean and how can i solve it??
plz help me
The error message is pretty clear. Somewhere within the
topology,
you have a "0" in the "type" column, which doesn't correspond
to any
known pair type.
-Justin
MOHIT KUMAR
Molecular Biochemistry & Biophysics
Graduate Student
Illinois Institute of Technology
Chicago,IL, USA
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
MOHIT KUMAR
Molecular Biochemistry & Biophysics
Graduate Student
Illinois Institute of Technology
Chicago,IL, USA
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
MOHIT KUMAR
Molecular Biochemistry & Biophysics
Graduate Student
Illinois Institute of Technology
Chicago,IL, USA
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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