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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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