VMD-L Mailing List

From: اسحاق خداپرست سیاهمزگی (issac.kh72_at_gmail.com)
Date: Wed Feb 20 2019 - 15:49:15 CST

Hi Josh
I didn't understand exactly what you mean.
Do you mean that VMD defines these coefficients (bonds, angles,
dihedrals,...) according to its own data? Without regard to the initial
data I have given?

then, is there any way to fix this problem?

Regards

Isaac

‫‪Vermaas, Joshua‬‏ <‪Joshua.Vermaas_at_nrel.gov‬‏> در تاریخ چهارشنبه ۲۰
فوریهٔ ۲۰۱۹ ساعت ۲۳:۲۰ نوشت:‬

> Hi Isaac,
>
> Guess dihedrals depends on the bond lists that exist within VMD. If
> something isn't bonded, topotools won't assign a dihedral, and I suspect
> that VMD isn't being given all the bonds that you expect to be there.
>
> -Josh
>
>
>
> On 2019-02-20 06:18:45-07:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> 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--000000000000f6d02005825a54f7--