[gmx-users] Query regarding the addition of solvent molecule

Justin Lemkul jalemkul at vt.edu
Tue Sep 9 13:29:16 CEST 2014 


On 9/9/14 7:09 AM, Christina Florina wrote:
> Hi,
>       Thanks for your suggestions.
>       If the .itp file has error, is there any other way to generate .itp
> files for the solvents or do i need to write them manually? Because the
> .itp files I have attached are generated using PRODRG. If I edit the
> chx.itp file based on the corrections you have told, will it be fine? I am
> getting the same error for all the 4 solvent files I have generated using
> PRODRG. I do not get the .itp and .gro files online or tutorials for the
> organic solvents i am using for my md studies.

The only problems I have ever had with PRODRG topologies are charges and charge 
groups.  If you fix those appropriately (charge groups being irrelevant if using 
the Verlet scheme in Gromacs), that's the only modification you should make.  I 
don't know where all that other stuff came from.

>      I have included the .itp file in both top directory and force field
> directory. It might be the reason the .gro file could be read in the
> solvate step. But how to make it in a correct format to proceed with?

Solvation doesn't depend on your custom topologies at all.

>      I am new to gromacs using other organic solvents apart from water and
> default solvents in gromacs package. So, kindly need help how to build an
> .itp file and .gro file for a solvent and to resolve the issue.
>

Make the changes I indicated in the last message.  Read Chapter 5 of the manual 
for explanations; all of the stuff I pointed out was either (1) syntactically 
incorrect or (2) not appropriate for the file format.

-Justin

> On Tue, Sep 9, 2014 at 3:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/9/14 12:51 AM, Christina Florina wrote:
>>
>>> Hi,
>>>         I have included the link to my dropbox where I have attached my
>>> gromacs topology files. Though I have included the cyclohexane itp file in
>>> the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO,
>>> Kindly need help in this regard.
>>>         Thank you in advance.
>>>
>>> https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0
>>>
>>>
>> You have several problems:
>>
>> 1. The #include statement for chx.itp is probably wrong (though I don't
>> know how you're organizing your files), but unless you've put chx.itp in
>> the force field directory, #include "gromos43a1.ff/chx.itp" is incorrect.
>>
>> 2. The contents of chx.itp are wrong for several reasons.  The #ifndef
>> lines are nonsensical and need to be deleted.  The #include statement for
>> water needs to be deleted.  The [system] and [molecules] levels (which are
>> system-level and thus can only go in a .top) need to be deleted.
>>
>>
>> -Justin
>>
>>   On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 9/5/14, 7:10 AM, Christina Florina wrote:
>>>>
>>>>   Hi,
>>>>>          I have included the chx.itp file in the protein.top file
>>>>> already.
>>>>> Checked with the molecule name (CHX) in the .itp file and also in the
>>>>> topology file variable name which matches CHX. But still I am getting
>>>>> the
>>>>> same error.
>>>>>          Kindly need help to resolve it.
>>>>>
>>>>>
>>>>>   Something doesn't add up.  You will need to provide all of your files
>>>> for
>>>> download via a file-sharing service to diagnose.  A simple #include
>>>> statement and correct updating of [molecules] is all that is needed.
>>>>
>>>> -Justin
>>>>
>>>>
>>>>
>>>>   On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> On 9/5/14, 2:50 AM, Christina Florina wrote:
>>>>>>
>>>>>>    Hi,
>>>>>>
>>>>>>>                 I have just started my work in MD and using Gromacs
>>>>>>> 5.0. I
>>>>>>> need
>>>>>>> to use cyclohexane as my solvent instead of water. I generated the
>>>>>>> topology
>>>>>>> file, .itp and .gro using PRODRG. I have successfully incorporated the
>>>>>>> .gro
>>>>>>> file using solvate command and generated the solvent box. But I am
>>>>>>> facing
>>>>>>> problem with grompp (ions.mdp) step before the addition of ions.
>>>>>>>
>>>>>>> gmx grompp -f ions.mdp -c protein_solv.gro -p protein.top -o ions.tpr
>>>>>>>
>>>>>>>                 I am getting the FATAL ERROR: NO SUCH MOLECULETYPE CHX
>>>>>>> though
>>>>>>> I have checked with the molecule name (CHX) in the cyclohexane .itp
>>>>>>> file.
>>>>>>> I
>>>>>>> have tired changing the name of the molecule also.
>>>>>>>
>>>>>>>                Do I need to add this cyclohexane solvent molecule in
>>>>>>> the
>>>>>>> forcefield file or .atp file, .rtp file? I tried adding them but still
>>>>>>> not
>>>>>>> able to run this. I might be incorrect while adding it in the .rtp
>>>>>>> file.
>>>>>>>
>>>>>>>                 So, I kindly need help regarding the addition of new
>>>>>>> solvent
>>>>>>> molecule in gromacs since I have other organic solvents also for my md
>>>>>>> work
>>>>>>> and having the same problem.
>>>>>>>
>>>>>>>
>>>>>>>    You need to #include the CHX .itp file in the system .top, and
>>>>>>> update
>>>>>>>
>>>>>> [molecules] accordingly.  Please note as well that PRODRG topologies
>>>>>> are
>>>>>> of
>>>>>> low quality in my experience and need to be corrected.  CHX is simple,
>>>>>> a
>>>>>> ring of CH2 atom types, all with zero charge.  Other results are less
>>>>>> trivial to fix.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>
>>>>>> Department of Pharmaceutical Sciences
>>>>>> School of Pharmacy
>>>>>> Health Sciences Facility II, Room 601
>>>>>> 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 601
>>>> 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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>>>> * Please search the archive at http://www.gromacs.org/
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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 601
>> 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
>>
>> * Please search the archive at http://www.gromacs.org/
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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 601
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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