Previous Thread
Next Thread
Print Thread
Page 1 of 3 1 2 3
#5043 01/17/05 09:19 AM
Joined: Sep 2004
Posts: 57
B
Baloo Offline OP
Forum Member
OP Offline
Forum Member
B
Joined: Sep 2004
Posts: 57
Dear All,

Has anyone come across the bond length, bond angle, torsion angle and phase values of Piperidine or Cyclohexane. Please guide me for the same.

Can these values be picked from the Proline parameters. I know that the piperidine or cyclohexane is not a planar structure.

Best Wishes..

Joined: Jan 2005
Posts: 127
P
Forum Member
Offline
Forum Member
P
Joined: Jan 2005
Posts: 127
Hello,

For cyclohexane, look into test/data/cyclohexane.str file available.

Dpending upon what conformation of cycloheaxne you want, try looking into , pickett and strauss paper in JACS or Stefan Fischer's (Harvard university) thesis or Fischer/Prof. Karplus papers. You can get all the information.

Hope this helps!
preeti

Joined: Sep 2004
Posts: 57
B
Baloo Offline OP
Forum Member
OP Offline
Forum Member
B
Joined: Sep 2004
Posts: 57
Hi Preeti,

Thanks for providing information. However could you please tell me where I will find cyclohexane.str file. As I donot find file with this name in /test/data directory

Best Wishes..

Joined: Jan 2005
Posts: 127
P
Forum Member
Offline
Forum Member
P
Joined: Jan 2005
Posts: 127
The file is located in "c30a1/test/data/" or "c31a1/test/data/" this is directory location where cyclohexane.str file is.

Joined: Oct 2003
Posts: 783
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 783
note that the standard charmm protein parameters will treat cyclohexane. you just need to create the residue in the topology file. piperdine will require some actual parameter development.

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Joined: Sep 2004
Posts: 57
B
Baloo Offline OP
Forum Member
OP Offline
Forum Member
B
Joined: Sep 2004
Posts: 57
i have measured the parameters for the cyclohexane after doing QM calculation and they donot match with standard charmm protein parameters. So i think one has to create and new atom type and assign the new values of parameters to that atom types for cyclohexane. The same holds true for piperidine.

best wishes..

Joined: Oct 2003
Posts: 783
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 783
remember that QM data is not necessarily correct! its just another model. alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Joined: Apr 2009
Posts: 22
Forum Member
Offline
Forum Member
Joined: Apr 2009
Posts: 22
Will they also work for cyclohexanone, or one should parameterize it by himself?

Joined: Sep 2003
Posts: 8,606
Likes: 24
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,606
Likes: 24
This is a fairly old post; you should be asking if new generalized small molecule FF supports cyclohexanone.


Rick Venable
computational chemist

Joined: Dec 2005
Posts: 1,535
Forum Member
Offline
Forum Member
Joined: Dec 2005
Posts: 1,535
As there isn't a lot of ring strain in cyclohexane, the general force field represents it with plain aliphatic carbon types and charges. You could probably make a cyclohexane model using atom types and parameters from the lipid FF and get very similar results.

Page 1 of 3 1 2 3

Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.009s Queries: 35 (0.004s) Memory: 0.7792 MB (Peak: 0.8698 MB) Data Comp: Off Server Time: 2022-10-05 19:08:47 UTC
Valid HTML 5 and Valid CSS