Previous Thread
Next Thread
Print Thread
Discrepancy of Nucleotide Parameters
#37908 06/05/20 02:49 AM
Joined: Jun 2020
Posts: 2
M
Mark_G Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Jun 2020
Posts: 2
Dear CHARMM Users,

I am using the CHARMM36 FF for DNA and RNA. par_all36_na.prm (downloaded from the sticky on this forum)
I noticed a discrepancy in the parameters for the LJ of carbon atoms in the sugars. The topology files identify these carbons as either CN7, or CN7B.
These are Sp3 carbons with a single hydrogen. The parameters for these atom types are given:

From par_all36_na.prm

CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1

When I examine the protein parameters I notice they are not equivalent to CT1, but CT.
This seems odd considering CT1 is an Sp3 carbon with a single hydrogen, the same as CN7 and CN7B.

From par_all36_prot.prm

CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 !
CT1 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane, 4/07, viv and adm jr.

However, they do match the CT1 atom type from par_all22_prot.prm

CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI

My question is, should I use the parameters as given or do I need to update the nucleotide parameters to the CHARMM36 protein CT1 found in par_all36_prot.prm?

Regards,
Mark

Re: Discrepancy of Nucleotide Parameters
Mark_G #37909 06/05/20 11:10 PM
Joined: Oct 2003
Posts: 781
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 781
Use the parameter as given. The are well tested in the context of nucleic acids as available in the file. The comment is probably a mistake from many years ago....

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: Discrepancy of Nucleotide Parameters
alex #37910 06/08/20 02:41 AM
Joined: Jun 2020
Posts: 2
M
Mark_G Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Jun 2020
Posts: 2
Thank you for the clarification.

Mark


Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.010s Queries: 20 (0.003s) Memory: 0.9024 MB (Peak: 0.9751 MB) Data Comp: Off Server Time: 2020-07-14 07:11:05 UTC
Valid HTML 5 and Valid CSS