On 11/19/19 5:55 AM, Bratin Kumar Das wrote:
Hi
I hope there is a problem in the topology...please follow the gromacs
tutorial..
More specifically: http://www.mdtutorials.com/gmx/complex/index.html
The #include statements are out of order. You cannot add new parameters
to the topology after any [moleculetype] has been declared. The entire
force field must be known before any species can be introduced.
-Justin
On Tue 19 Nov, 2019, 3:34 PM Alessandra Villa, <
[email protected]> wrote:
Hi,
Pls note that the maillist does not support attachments.
Also it will better/helpful to use emails subject.
Kind regards
Alessandra
On Tue, Nov 19, 2019 at 10:46 AM pooja kesari <[email protected]>
wrote:
Dear All,
I am doing a protein-ligand simulation, when i was try to *add ions to
the
system*
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
*there was an error*
Fatal error:
Syntax error - File lig.prm, line 2
Last line read:
'[ bondtypes ]'
Invalid order for directive bondtypes
*my topol.top- ligand defination is as follows *
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include ligand parameters
#include "lig.prm"
; Include ligand topology
#include "lig.itp"
; Include water topology
#include "./charmm36-mar2019.ff/tip3p.itp"
I have included the ligand parameter details as suggested in lig.top file
generated by cgenff python script. I have attached the itp and prm file
for
reference.
Thanks & Regards,
Dr. Pooja Kesari
Post Doctoral Fellow
Department Of Biosciences and Bioengineering
Indian Institute of Technology Bombay
INDIA
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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