[gmx-users] how to convert CGenFF into .itp file?

[Albert]

On 12/26/2012 07:53 PM, David van der Spoel wrote:
> Hey, it's open source. Let us know how it goes 

you can simple create an account and login

https://www.paramchem.org/

after your login, click "upload molecule" in left panel. Now you will 
see the option:

"Include parameters that are already in CGenFF"

tick this option and the server will generate a full version of ligand 
topology  which could be  independent from the offline CGenFF. Now what 
we need is just improve the script and convert it into a single .itp 
file into Gromacs. I think this would be the best solution.

Here is an example output for Methanol molecule from CGenFF


------------------example--------------------------------------------------------------------------

* Toppar stream file generated by
* CHARMM General Force Field (CGenFF) program version 0.9.6 beta
* For use with CGenFF version 2b7
*

read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 0.9.6 beta
*
36 1

! "penalty" is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

RESI 887            0.000 ! param penalty=   0.000 ; charge penalty=   0.000
GROUP            ! CHARGE   CH_PENALTY
ATOM O      OG311  -0.651 !    0.000
ATOM C      CG331  -0.039 !    0.000
ATOM H1     HGA3    0.090 !    0.000
ATOM H2     HGA3    0.090 !    0.000
ATOM H3     HGA3    0.090 !    0.000
ATOM H4     HGP1    0.420 !    0.000

BOND O    C
BOND O    H4
BOND C    H1
BOND C    H2
BOND C    H3

END

read param card flex append
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 0.9.6 beta
*

! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

BONDS
CG331  OG311   428.00     1.4200 ! PROT methanol vib fit EMB 11/21/89
CG331  HGA3    322.00     1.1110 ! PROT alkane update, adm jr., 3/2/92
OG311  HGP1    545.00     0.9600 ! PROT EMB 11/21/89 methanol vib fit; og tested on MeOH EtOH,...

ANGLES
OG311  CG331  HGA3     45.90    108.89 ! PROT MeOH, EMB, 10/10/89
HGA3   CG331  HGA3     35.50    108.40    5.40   1.80200 ! PROT alkane update, adm jr., 3/2/92
CG331  OG311  HGP1     57.50    106.00 ! Team Sugar, HCP1M OC311M CC331M; unchanged

DIHEDRALS
HGA3   CG331  OG311  HGP1       0.1800  3     0.00 ! og methanol

IMPROPERS

END
RETURN