[gmx-users] miscelle formation using ligands only
Chetan Puri
chetanpuris at gmail.com
Wed Sep 16 17:01:47 CEST 2015
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 .
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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> 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
>>>
>>> ==================================================
>>> --
>>> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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