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

[Christina Florina]

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

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
>>>>>
>>>>>