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

[Justin Lemkul]

On 9/9/14 9:41 AM, Christina Florina wrote:
> Hi,
>       Thank you for the suggestions. I did the modifications in the .itp
> file and the grompp step generated the .tpr file successfully.
>       But now, I am facing problem in the genion step, while adding the NA
> ions the group 13 (usually SOL for water solvent) is not present there. If
> I select anyother group like system (Grp-1) its showing some fatal error
> which is not present in gromacs errors and documentation. I have attached
> the screenshot of the error page (terminal) and the new .itp file
> (modified) for your reference.
>       Do I need to add the cyclohexane molecule (CHX) in any of the
> directories to resolve this error? Kindly need help.
>
>
> https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0
>

There's no water in your system to replace:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
CHX              3414

I suggest you refer to some tutorial material to understand normal Gromacs 
workflows and topology organization.  There are many linked from the Gromacs 
website, some of which involve building system with complex/non-water solvents.

-Justin

> On Tue, Sep 9, 2014 at 4:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>>>>>
>>>>>>

-- 
==================================================

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

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