Previous Thread
Next Thread
Print Thread
Why "No angle parameters for ( OT HT HT )"
#4068 11/05/04 08:40 PM
Joined: Oct 2004
Posts: 32
M
MDM Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Oct 2004
Posts: 32
Dear all,

When I read a water molecule as TIP3 and use par_all22, why the charmm complains "No angle parameters for ( OT HT HT)", I notice in par_all22, angle (HT OT HT) had been defined. Could anyone give me some clue?

Thanks,
MDM

------------------------------------------------
CHARMM> open unit 10 read form name /carlsbad/wat.pdb
VOPEN> Attempting to open::/carlsbad/wat.pdb::
OPNLGU> Unit 10 opened for READONLY access to /carlsbad/wat.pdb

CHARMM> read sequ pdb unit 10
MAINIO> Sequence information being read from unit 10.
TITLE> *

RESIDUE SEQUENCE -- 1 RESIDUES
CHARMM> GENE WAT SETUP WARN
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
: No angle parameters for 3 ( OT HT HT )
: No angle parameters for 4 ( OT HT HT )
: A TOTAL OF 2 MISSING PARAMETERS

***** LEVEL -1 WARNING FROM *****
***** CODES> MISSING PARAMETERS
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5
.........................................................

Re: Why "No angle parameters for ( OT HT HT )"
MDM #4069 11/05/04 08:58 PM
Joined: Sep 2003
Posts: 4,797
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,797
Likes: 2
You should use the following form for the generate statement (as is shown in all example files with TIP3P water):
gene wat noangle

TIP3P is treated as a rigid molecule (using SHAKE) so the angle parameters are not needed - if you omit NOANGLE in the generate command, CHARMM automatically generates all angles, which in this case is not the wanted behavior.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Why "No angle parameters for ( OT HT HT )"
MDM #4070 11/05/04 09:11 PM
Joined: Oct 2004
Posts: 32
M
MDM Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Oct 2004
Posts: 32
Well, if I need a FLEXIBLE water molecule, I definitely can not use TIP3. What is best choice then? TP3M?

Thanks,
MDM

Re: Why "No angle parameters for ( OT HT HT )"
MDM #4071 11/05/04 10:19 PM
Joined: Sep 2003
Posts: 8,506
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,506
TP3M is just TIP3 with some changes to support the Merck force field.

All CHARMM macromolecule parameters have been developed with respect to TIP3, which is a rigid water molecule as originally developed by Jorgensen.


Rick Venable
computational chemist


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: 0.012s Queries: 22 (0.006s) Memory: 0.9127 MB (Peak: 0.9943 MB) Data Comp: Off Server Time: 2020-10-30 01:49:57 UTC
Valid HTML 5 and Valid CSS