Previous Thread
Next Thread
Print Thread
Conversion of OPLS ITP file to charmm/gromacs itp file
#38202 02/25/21 03:18 PM
Joined: Sep 2019
Posts: 2
Y
yogesh Offline OP
Forum Member
OP Offline
Forum Member
Y
Joined: Sep 2019
Posts: 2
greetings users,

I have generated an gromacs compatible ff for a ligand from LIGPargen.
ITP is in OPLS ff format having sections as follows.
; GENERATED BY LigParGen Server
;
[ atomtypes ]
[ moleculetype ]
[ atoms ]
[ bonds ]
[ angles ]
[ dihedrals ]
**; IMPROPER DIHEDRAL ANGLES **
[ dihedrals ]
; PROPER DIHEDRAL ANGLES
[ pairs ]

I want to convert the parameters to gromacs compatible charmm FF. this FF require sections like

CHARMM36 FF in GROMACS format

[ defaults ]
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
** [ bondtypes ]**
[ angletypes ]
; i j k func th0 cth S0 Kub
[ dihedraltypes ]
; i j k l func phi0 cp mult
can someone suggest way to interconvert the parameters?
I will be really thankful for your help.

Re: Conversion of OPLS ITP file to charmm/gromacs itp file
yogesh #38205 02/25/21 06:49 PM
Joined: Sep 2003
Posts: 4,817
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,817
Likes: 2
OPLS is not CHARMM
ITP/GROMACS is also not CHARMM
This, however, is a CHARMM forum.
Please ask your question in a relevant forum

Scientifically: If you intend to run a simulation using the CHARMM36 force field for your protein or whatever together with a ligand parameterized to for the OPLS force field (if that is what LIGPargen does) you should be prepared to answer questions from manuscript reviewers about this strategy.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Conversion of OPLS ITP file to charmm/gromacs itp file
yogesh #38206 02/25/21 08:05 PM
Joined: Sep 2003
Posts: 8,543
Likes: 3
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,543
Likes: 3
Right, if you're using the CHARMM FF for most molecules, it would make more sense to use the CGenFF server to add another molecule.


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: 0.013s Queries: 20 (0.008s) Memory: 0.9044 MB (Peak: 0.9778 MB) Data Comp: Off Server Time: 2021-04-20 23:31:35 UTC
Valid HTML 5 and Valid CSS