[gmx-users] miscelle formation using ligands only

Wed Sep 16 13:50:42 CEST 2015

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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>> --
>> ==================================================
>>
>> 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

==================================================