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

[Christina Florina]

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

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
>
> ==================================================
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> Gromacs Users mailing list
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