VMD-L Mailing List

From: اسحاق خداپرست سیاهمزگی (issac.kh72_at_gmail.com)
Date: Wed Feb 20 2019 - 02:33:51 CST

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.
>>>>
>>>