[gmx-users] (no subject)

[Justin Lemkul]

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
>>>>
>>>> ==================================================
>>>>
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>>>> 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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>> posting!
>>
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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

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