[gmx-users] (no subject)

[Justin Lemkul]

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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>

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

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

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