[gmx-users] miscelle formation using ligands only

[Chetan Puri]

thanks for you help and today i was able to solve the problem,
actually my pdb file was made using packmole for 5 molecules and molecules
were prepared using prodrug , so my pdb file contained names of DRG A,
B,C,D,E
and i tried to change it to  SC3,CA1,D3G,......... in the last packed PDB
file and also i made changes in the itp files. So in my topolgy prepared
file also i used the same names under molecules part. As a result of this
the grompp was not able to read my .itp files and showed error as too few
parameters on line. But then again i kept the  names as such and included
DRG_chain_A,B,C ....... names in my topology file molecules part and
also.itp molecule name . There after grompp was able to read all the files.
I received two notes :
note1 was for verlet scheme >10 and for gpu >20 .............
note2 was for some PME load distribution
I have used ions.mdp file of the tutorial just to make .tpr file.
i hope this is of not great concern and i would also like to know that why
was grompp not able to read itp files even though i have placed the same
name in every file.


On Mon, Sep 14, 2015 at 10:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/14/15 11:18 AM, Chetan Puri wrote:
>
>> i tried to prepare a topolgy file for my ligands and it contained
>> following
>> things,
>> #include "gromos43a1.ff/forcefield.itp"
>> #include "drg1.itp"
>> #include"drg2.itp"
>> #include"drg3.itp"
>> #include "gromos43a1.ff/spc.itp"
>>
>> [system]
>> miscelle
>> [molecules]
>> drg1        8
>> drg2         5
>> drg3         7
>> sol           363408
>>
>>
>> But since i have packed the system using PACKMOL intially there were some
>> error that no. of coordintaes of gro and top file are not matching since
>> intially i took no. of molecules as one for each type but later upon
>> changing to the no. as in my packmol input that error had gone and new
>> error is showing up
>> i.e. Too few parameters in line 1 for drg2.itp
>>         Too few parameters in line 1 for drg3.itp
>>
>> and if i override it with maxwarn than i saw that all the ligands were
>> stuck together at one place and also with some different representation .
>>
>>
> Don't blow past error messages with -maxwarn.  It is extremely dangerous
> and unless you have specific knowledge that the problem is not important,
> don't use it.
>
> The error messages indicate that the contents of drg2.itp and drg3.itp are
> incorrect or misformatted (or perhaps that the lack of a space between
> #include and the file name is causing a problem, but that's just
> speculation).
>
> so can you please help me out with this thing and also is there any other
>> way by using gromacs and packing a system of different ligands (gromacs
>> version 5.0.4)
>>
>>
> gmx insert-molecules can be used to add small molecules into a system, but
> if it's already built, why bother?
>
> If you want to rebuild the system for any reason, see:
>
> http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
>
> If you want commentary on the contents of your .itp files, you will need
> to upload them to a file-sharing service and provide the URL.  Otherwise,
> we're working blind and that is not productive for anyone.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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