[gmx-users] (no subject)

[Justin Lemkul]

On 8/26/19 2:33 PM, Navneet Kumar Singh wrote:
> I can't understand meaning of this "For all other GROMACS versions, you
> will have to manually edit the topology to use "3fad" construction and
> appropriate atom numbers." If I am using version other than the
> Gromacs2016.x.
>
> Can I get example of any topology file where these kind of construction've
> for loan pair done manually in the topology file?

Please see the manual for examples of what the different construction 
types are.

-Justin

> On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
>>> Do I have to add vsite3 information from unk.itp to system.top files?
>> That directive belongs in the topology to which it corresponds. If it is
>> in unk.itp, then it is already in system.top. You don't need to include
>> anything else.
>>
>> -Justin
>>
>>> -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
>>>
>>> On Mon, 26 Aug 2019, 00:58 Justin Lemkul, <jalemkul at vt.edu> wrote:
>>>
>>>> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
>>>>> Yeah! I have read that.
>>>>>
>>>>> uses -maxwarn 1 to produce .tpr file using grompp command as mentioned
>> in
>>>> Since you are getting an error rather than a warning, that means you are
>>>> not using GROMACS 2016.x, as the instructions I pointed to you say.
>>>>
>>>> If you want to use a different GROMACS version, you have to change the
>>>> topology. Again see the link I provided for a description of what to do.
>>>>
>>>> -Justin
>>>>
>>>>> python script cgenff_charmm2gmx_py2.py
>>>>>
>>>>> output of cgenff_charmm2gmx_py2.py
>>>>>
>> _____________________________________________________________________________________________________________________________________________________________
>>>>> NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,
>>>> Mar
>>>>> 26 2019, 10:00:46)
>>>>> [GCC 5.4.0 20160609]
>>>>>
>>>>> NOTE 2: Please be sure to use the same version of CGenFF in your
>>>>> simulations that was used during parameter generation:
>>>>> --Version of CGenFF detected in  unk.str : 4.0
>>>>> --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :
>> 4.0
>>>>> NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
>>>>> parameters that are already in CGenFF' option when uploading a molecule
>>>>> into CGenFF.
>>>>>
>>>>> NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
>>>> This
>>>>> is not a problem, just FYI!
>>>>>
>>>>> ============ DONE ============
>>>>> Conversion complete.
>>>>> The molecule topology has been written to unk.itp
>>>>> Additional parameters needed by the molecule are written to unk.prm,
>>>> which
>>>>> needs to be included in the system .top
>>>>>
>>>>> PLEASE NOTE: lone pair construction requires duplicate host atom
>> numbers,
>>>>> which will make grompp complain
>>>>> To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this
>>>> check
>>>>
>> ________________________________________________________________________________________________________________________________________________________________
>>>>> After that I am using same -maxwarn 1 but still, it's giving error. It
>>>> may
>>>>> be some silly mistake please let me know.
>>>>>
>>>>>
>>>>> On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
>>>>>>> Thank You Sir!
>>>>>>>
>>>>>>> Attached file can be downloaded from following link.
>>>>>>>
>>>>>>> https://fil.email/OR7Nsh0f
>>>>>>> <https://fil.email/OR7Nsh0f?&showconfirmation=true>
>>>>>>> ____________________________________________________________________
>>>>>>> Error
>>>>>>>
>>>>>>> ERROR 1 [file unk.itp, line 497]:
>>>>>>>       Duplicate atom index (23) in virtual_sites3
>>>>>>> ___________________________________________________________________
>>>>>>>
>>>>>>> It support lone pair construction for halogens only. Please suggest
>>>> some
>>>>>>> alternatives.
>>>>>> The link I provided before describes what you need to do. Please
>> consult
>>>>>> that information.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Assistant Professor
>>>>>> Office: 301 Fralin Hall
>>>>>> Lab: 303 Engel Hall
>>>>>>
>>>>>> Virginia Tech Department of Biochemistry
>>>>>> 340 West Campus Dr.
>>>>>> Blacksburg, VA 24061
>>>>>>
>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>> http://www.thelemkullab.com
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
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>>>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Office: 301 Fralin Hall
>>>> Lab: 303 Engel Hall
>>>>
>>>> Virginia Tech Department of Biochemistry
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> send a mail to gmx-users-request at gromacs.org.
>>
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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