[gmx-users] miscelle formation using ligands only
Justin Lemkul
jalemkul at vt.edu
Wed Sep 16 17:53:14 CEST 2015
On 9/16/15 11:01 AM, Chetan Puri wrote:
> thanks for the suggestion ,
> I used semi-empirical nddo method for charge determination of each
> molecules and found out that there was huge difference between the charges
> provided by the prodrug and that calculated by semi-empirical nddo method.
> So can i modify the charges in the .itp file of various molecules and use
> it .
>
You should probably do some more reading about the GROMOS force fields before
diving into this. There is a minimal, at best, connection between QM and
GROMOS, unlike AMBER and CHARMM, which are closely linked to QM. GROMOS
parametrization is highly empirical and targets condensed phase data without any
real reliance on QM (aside from possibly only a very basic approximation of
charge distribution).
-Justin
> On Wed, Sep 16, 2015 at 5:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/15/15 11:01 PM, Chetan Puri wrote:
>>
>>> so what is the best option for topologies.
>>>
>>>
>> A force field you trust in concert with molecules that are individually
>> parametrized using suitable target data. There is a reason why
>> parametrization is considered an expert topic. While there are numerous
>> web servers that will give you topologies for GROMOS, AMBER, and CHARMM, it
>> is incumbent on the user to verify the topologies against any available
>> target data and refine/reparametrize as needed based on the findings of
>> those assessments. Nothing should be trusted blindly, from any source.
>>
>> -Justin
>>
>>
>> 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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>>>>>> Gromacs Users mailing list
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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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>>>> Gromacs Users mailing list
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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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>> Gromacs Users mailing list
>>
>> * Please search the archive at
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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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