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

[David van der Spoel]

On 2012-12-26 20:29, Albert wrote:
> On 12/26/2012 07:53 PM, David van der Spoel wrote:
>> Hey, it's open source. Let us know how it goes
>

Sorry what I meant was: If you make a better version of the 
charmm2gromacs script, then please upload it to the website.

Cheers, David.
> 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
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se