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

[Justin Lemkul]

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

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

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