Olga Ivchenko wrote:
Dear All,
I just want to know if the programm PRODRG is able to generate for my
ligand files with .top extension.
No, but it is trivial to interconvert .itp and .top manually:
http://www.gromacs.org/Documentation/File_Formats/.itp_File
-Justin
I have two files one is itp format and other is gro using PRODRG.
If it is possible what is the name here
:http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta#DRGFIN.GRO
Yours sincerely,
Olga
2010/11/10 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Olga Ivchenko wrote:
Dear All,
I have created creating topology file using *prodrg_beta (using
gromos 96 ff)
<http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta>*. When I
am trying to run energy minimization it writes an error:
Please consider carefully the caveats about PRODRG noted here
(second paragraph):
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
Syntax error - File creatine.top, line 19
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype
I looked at previoust mailing lists according this problem. I
can not find direct answer.
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults
Somehow you've cut and pasted such that you've got a [moleculetype]
directive out of order.
I tried to add this line in the topology file
#include "ffG43a1.ff/DRGGMX.itp"
An again an error:Fatal error:
Topology include file "ffG43a1.ff/DRGGMX.itp" not found
Then either the file doesn't exist or isn't within the search path
grompp is trying.
-Justin
Please can you advice me on this.
Yours sincerely,
Olga
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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