[gmx-users] miscelle formation using ligands only

[Chetan Puri]

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 .

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)



On Sun, Sep 13, 2015 at 6:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/13/15 3:47 AM, Chetan Puri wrote:
>
>> So it means that my topology file should not contain any heading such as
>> bonds, atoms, dihedral, and should only contain #include drug.itp of
>> various molecules with system name and number of various molecules.
>>
>
> That's likely the best route, though you can approach it a number of
> ways.  For a system that is simply a mixture of small molecules, I think
> this is the cleanest approach, though.
>
> Can I just make a box of water.pdb using packmol and use pdb2gmx to
>> generategenerate a topology with oplsa.ff and include drug.itp files in
>> that topology file.
>>
>>
> You can, but it's really trivial to do yourself without pdb2gmx:
>
> #include "oplsaa.ff/forcefield.itp"
> #include "oplsaa.ff/tip3p.itp"
>
> [ system ]
> water
>
> [ molecules ]
> SOL     X
>
> where X is the number of molecules you have. That's all there is to it.
>
> -Justin
>
>
> On Sunday, September 13, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 9/11/15 11:59 PM, Chetan Puri wrote:
>>>
>>>>
>>>> I am using gromacs for the first time . I have installed gromacs 5.0.4
>>>> version and i want to check a miscelle is formed or not using 5
>>>> different
>>>>    ligands in different ratios. I have gone through all basic tutorials
>>>> on
>>>> how to use gromacs ( lysosyme,protein-ligand).
>>>>
>>>> But i am stuck with the problem of having ligands only for simulation
>>>> due
>>>> to no force field and topology file.
>>>>                         I have tried to use packmol to pack a cubic box
>>>>
>>> with
>>
>>> all my different ligands in different ratios and generated a pdb file but
>>>> without making a topology file i am stuck.
>>>>             So if some one can suggest some possible ways  of doing it
>>>>
>>> and i
>>
>>> don't have much computational background of manipulating various file
>>>> extensions of gromacs.
>>>>
>>>>
>>> The only difference here is that you probably aren't going to be using
>>>
>> pdb2gmx, so your topology will be one of your own creation.  In practice,
>> the .top is probably just going to amount to a series of #include
>> statements for the topologies of the various molecules you want to study.
>>
>>>
>>> -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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>>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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