VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Feb 20 2019 - 13:50:35 CST

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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.