From: اسحاق خداپرست سیاهمزگی (issac.kh72_at_gmail.com)
Date: Wed Feb 20 2019 - 02:45:56 CST

Hello Dr. Axel

Excuse me.
I did not intend to annoy you. I thought you did not see my previous
message.

Best Regards

Isaac

‫‪Axel Kohlmeyer‬‏ <‪akohlmey_at_gmail.com‬‏> در تاریخ چهارشنبه ۲۰ فوریهٔ ۲۰۱۹
ساعت ۱۵:۴۲ نوشت:‬

> 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.
>>>>>>
>>>>>