[gmx-users] miscelle formation using ligands only

Wed Sep 16 05:01:20 CEST 2015

 so what is the best option for topologies.

On Wed, Sep 16, 2015 at 2:19 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/15/15 11:35 AM, Chetan Puri wrote:
>
>> 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
>>
>
> PRODRG produces notoriously bad parameters.  Don't use those topologies
> directly and expect good results.
>
> 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.
>>
>>
> Your description is too confusing to be able to provide useful.  There's
> nothing anyone can actually do to help you without actual commands, files,
> and real error messages, rather than what you're filtering through your
> thoughts.
>
> Sounds like you've hacked together a solution, though, so hopefully
> everything matches up.  But like I said above, PRODRG topologies are not
> reliable and reviewers should criticize their use heavily.  The problems
> are well known.
>
> -Justin
>
>
>
>> 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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>>>
> --
> ==================================================
>
> 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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