VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Feb 20 2019 - 06:12:00 CST

I am no magician and am providing support for topotools in my free time.
When I have no free time, it will take some time to evaluate and debug
issues.

Axel 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
On Wed, Feb 20, 2019, 07:04 اسحاق خداپرست سیاهمزگی <issac.kh72_at_gmail.com>
wrote:
> Hello Dr. Axel
>
> I didn't receive any answer to my question. Can you tell me what should I
> do to solve this problem?
>
> Regards
>
> Isaac
>
> ‫اسحاق خداپرست سیاهمزگی <‪issac.kh72_at_gmail.com‬‏> در تاریخ سه‌شنبه ۱۹
> فوریهٔ ۲۰۱۹ ساعت ۱۲:۴۹ نوشت:‬
>
>> I want to use CHARMM forcefield. because i want to add water and DNA
>> molecule to GO .
>>
>>
>> ‫‪Axel Kohlmeyer‬‏ <‪akohlmey_at_gmail.com‬‏> در تاریخ سه‌شنبه ۱۹ فوریهٔ
>> ۲۰۱۹ ساعت ۱۱:۳۰ نوشت:‬
>>
>>> One more question. Which force field do you want to use with the
>>> resulting data file?
>>>
>>> Axel
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>> On Tue, Feb 19, 2019, 07:54 اسحاق خداپرست سیاهمزگی <issac.kh72_at_gmail.com
>>> wrote:
>>>
>>>> Dear Axel
>>>>
>>>> I can make graphene with VMD but I want to make a graphene-oxide .so i
>>>> wrote a c++ programm which make a GO .xyz file. then i used VMD to make
>>>> it's .pdb file and at the end i used topo tools as i said before.
>>>>
>>>> now i attached .xyz and .pdb files that i used.
>>>>
>>>> Regards
>>>>
>>>> Isaac
>>>>
>>>>
>>>> ‫‪Axel Kohlmeyer‬‏ <‪akohlmey_at_gmail.com‬‏> در تاریخ دوشنبه ۱۸ فوریهٔ
>>>> ۲۰۱۹ ساعت ۲۲:۴۴ نوشت:‬
>>>>
>>>>> you didn't report tbe topotools version
>>>>> the data file itself is useless without the original file that you
>>>>> used.
>>>>>
>>>>> you know that you can build a proper graphene structure directly from
>>>>> within VMD, right?
>>>>>
>>>>> axel.
>>>>>
>>>>> ‪On Mon, Feb 18, 2019 at 1:11 PM ‫اسحاق خداپرست سیاهمزگی‬‎ <
>>>>> issac.kh72_at_gmail.com> wrote:‬
>>>>>
>>>>>> Hi Dr. Axel
>>>>>>
>>>>>> I used VMD for LINUXAMD64, version 1.9.4a12 (December 21, 2017).
>>>>>> first i made an xyz file. then i used VMD and chnged its format to
>>>>>> pdb. after that i used topo tools of VMD with this commands:
>>>>>> {
>>>>>> topo retypebonds
>>>>>> topo guessangles
>>>>>> topo guessdihedrals
>>>>>> topo guessimpropers
>>>>>> topo writelammpsdata graphene.data full
>>>>>> }
>>>>>> I checked my data for a small structure. the results were the same.
>>>>>> My reason for wrong dihedrals is that it defines same dihedrals(for
>>>>>> example):
>>>>>>
>>>>>> ID          dihedral-type atom1 atom2 atom3 atom4
>>>>>> 6             3                 1         2        4        3        *
>>>>>> 7             3                 3         2        4        3
>>>>>> 8             1                 1         2        3        5
>>>>>> 9             2                 1         2        3        4        *
>>>>>>
>>>>>> and
>>>>>>
>>>>>> same atom in one dihedral(for example):
>>>>>>
>>>>>> ID         dihedral-type atom1 atom2 atom3 atom4
>>>>>> 49          3                  *10*       9        11       *10*
>>>>>>
>>>>>> *I attached my datafile with this mail.*
>>>>>>
>>>>>> Regards
>>>>>>
>>>>>> Isaac
>>>>>>
>>>>>> ‫‪Axel Kohlmeyer‬‏ <‪akohlmey_at_gmail.com‬‏> در تاریخ دوشنبه ۱۸ فوریهٔ
>>>>>> ۲۰۱۹ ساعت ۱۸:۱۶ نوشت:‬
>>>>>>
>>>>>>> You are making some strong statements here. A) how do you determine,
>>>>>>> that the dihedrals are guessed "wrong"? B) what does "wrong" mean? Not what
>>>>>>> you want or not what the algorithm says? C) you don't provide any proof or
>>>>>>> details of an error, so how can somebody suggest a correction? And finally
>>>>>>> D) did you provide correct bond information? If yes how?
>>>>>>>
>>>>>>> Also, always name the version of vmd and topotools you are using.
>>>>>>>
>>>>>>> Axel
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
>>>>>>> College of Science & Technology, Temple University, Philadelphia PA,
>>>>>>> USA
>>>>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>>>>
>>>>>>> On Mon, Feb 18, 2019, 14:31 اسحاق خداپرست سیاهمزگی <
>>>>>>> issac.kh72_at_gmail.com wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi
>>>>>>>> I used topo tools for writing lammps datafile. But this tools makes
>>>>>>>> some wrong dihedrals. Is there any way to fix this error?
>>>>>>>> Thanks
>>>>>>>> Isaac
>>>>>>>>
>>>>>>>
>>>>>
>>>>> --
>>>>> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
>>>>> College of Science & Technology, Temple University, Philadelphia PA,
>>>>> USA
>>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>>
>>>>