[gmx-users] (no subject)

[Justin Lemkul]

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, <
> alessandra.villa.biosim at gmail.com> 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 <poojakesari10 at gmail.com>
>> 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
>>> --
>>> Gromacs Users mailing list
>>>
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>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================