Previous Thread
Next Thread
Print Thread
#36563 08/16/17 03:55 PM
Joined: Aug 2017
Posts: 3
M
Mitra Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Aug 2017
Posts: 3
Hello everyone,

I am currently working on my bachelor thesis and have a question about the topology file top_all36_prot.rtf:
I do not understand how I can get the bond length and bond angle for Pres atoms.
For example CTER looks like this:

PRES CTER -1.00 ! standard C-terminus
GROUP ! use in generate statement
ATOM C CC 0.34 ! OT2(-)
ATOM OT1 OC -0.67 ! /
ATOM OT2 OC -0.67 ! -C
DELETE ATOM O ! \\
BOND C OT2 ! OT1
DOUBLE C OT1
IMPR C CA OT2 OT1
ACCEPTOR OT1 C
ACCEPTOR OT2 C
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000

I get that CNEU is not standing alone but has to be seen in relation with the amino acid residues and for N CA for example I could use the bond length of the amino acid. But that still leaves OT2 without information. Where do I get those values?

I would really appreciate if someone could show me an example between CTER and GLY or an other amino acid...

Thanks in advance and best regards,
Mitra

Joined: Sep 2003
Posts: 8,629
Likes: 24
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,629
Likes: 24
Do you just want the values, or are you having problems with IC BUILD?

The actual equilibrium values are in the parameter file, in the BONDS and ANGLES sections; the values in the IC entries for e.g. ASP should be fairly close.

For IC BUILD issues, one needs to use the SETUP keyword with any GENErate or PATCH statements, and then use the IC PARAM command, which fills in any zero values for bonds and angles in an IC entry with the equilibrium values from the parameters. If most of the atoms have coordinates, e.g. an imported PDB file, then IC FILL is advised. I have several posts in the Script Archive which demonstrate coordinate import in detail.


Rick Venable
computational chemist

Joined: Aug 2017
Posts: 3
M
Mitra Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Aug 2017
Posts: 3
Thanks for the fast answer.

I want the values for another program which uses a different parameter format. So, I have to translate Charmm into the other format but that is hard if I can not understand the Charmm file. That is why I asked for an example.

Joined: Sep 2003
Posts: 8,629
Likes: 24
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,629
Likes: 24
Note that the IC entry values are only used for model building, and do not otherwise impact energy calculations.

The equilibrium values and force constants for the bonds and angles are in the parameter file, i.e. par_all36_prot.prm

See the CHARMM documentation files rtop.doc, parmfile.doc, and io.doc for detailed information on these file formats.


Rick Venable
computational chemist

Joined: Aug 2017
Posts: 3
M
Mitra Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Aug 2017
Posts: 3
Thanks for the answer! I think I got it now. smile


Moderated by  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~deb10u2 Page Time: 0.012s Queries: 24 (0.008s) Memory: 0.7455 MB (Peak: 0.7990 MB) Data Comp: Off Server Time: 2023-01-27 08:59:43 UTC
Valid HTML 5 and Valid CSS