[gmx-users] Query regarding the addition of solvent molecule
Christina Florina
rouvier.florina at gmail.com
Thu Sep 11 14:49:07 CEST 2014
Hi,
[ molecules ]
; Compound #mols
Protein_chain_A 1
CHX 3414
Here no water molecules to replace but to neutralize the system I
need to replace the solvent ions. As you told I went through the tutorial
regarding the genion and addition of ions, but to neutralize solvents apart
from water(SOL) I couldnt find enough details. I tried with methanol, then
I got Group 13 (MeOH) (instead of SOL) to replace the solvents with the
ions in the genion step. But with the solvents I am using like cyclohexane,
I am getting only 9 groups and if I try to choose any group its showing
error as follows:
*Your solvent group size (23449) is not a multiple of 8*
I don't know how to resolve this error though I have modified the
topology file (.top) with the no. of ions. Kindly need help with this
issue. I have attached the screenshot of the error page in the link below.
https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0
Thank you.
On Tue, Sep 9, 2014 at 9:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ==================================================
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