Dinamica molecular

TEST CCgenFF with Bencene molecule

Este es un test del uso de CCgenFF con una molecula simple de benceno.

Antes se utilizo esta herramienta pero presento problemas, retomare para ver si he pasado por alto algunos detalles que antes desconocia.

 

Lo primero que pide es una molecula en formato .mol2 con todos los hidrogenos agregados, esto lo realice con UCSF Chimera 1.14

@<TRIPOS>MOLECULE
ligand_wH.pdb
12 12 1 0 0
SMALL
NO_CHARGES

@<TRIPOS>ATOM
1 C1 -32.9690 6.1960 2.8770 C.ar 1 BNZ 0.0000
2 C2 -32.9450 7.0460 3.9730 C.ar 1 BNZ 0.0000
3 C3 -33.7190 6.7980 5.1130 C.ar 1 BNZ 0.0000
4 C4 -34.5400 5.6800 5.1430 C.ar 1 BNZ 0.0000
5 C5 -34.5450 4.8250 4.0440 C.ar 1 BNZ 0.0000
6 C6 -33.7870 5.0690 2.9150 C.ar 1 BNZ 0.0000
7 H1 -32.3630 6.4050 2.0080 H 1 BNZ 0.0000
8 H2 -32.3130 7.9210 3.9460 H 1 BNZ 0.0000
9 H3 -33.6770 7.4690 5.9590 H 1 BNZ 0.0000
10 H4 -35.1630 5.4770 6.0020 H 1 BNZ 0.0000
11 H5 -35.1630 3.9400 4.0750 H 1 BNZ 0.0000
12 H6 -33.8280 4.3950 2.0730 H 1 BNZ 0.0000
@<TRIPOS>BOND
1 1 2 ar
2 1 6 ar
3 1 7 1
4 2 3 ar
5 2 8 1
6 3 4 ar
7 3 9 1
8 4 5 ar
9 4 10 1
10 5 6 ar
11 5 11 1
12 6 12 1
@<TRIPOS>SUBSTRUCTURE
1 BNZ 1 RESIDUE 4 A BNZ 0 ROOT

Se conservan las coordenadas del ejemplo con LigParGen


Primer detalle, sino se marca la segunda casilla, No darla los valores de BONDS  ANGLES DIHEDRALS IMPROPERS

This check box causes parameter lines to be copied verbatim from the main CGenFF parameter fileThe copied parameters will not have a PENALTY score, in contrast to the ones that were guessed by analogy. As explained in the summary of output data and its utilization, paramchem.org’s CHARMM-compatible “stream files” are meant to be read into your molecular simulation program after reading the CHARMM General Force Field (CGenFF); basic examples showing how to do so can be found here. When following these instructions, the only effect of checking the “Include parameters that are already in CGenFF” box is to trigger “duplicate parameter” warnings. Because some MD codes don’t handle duplicate dihedral parameters correctly, we cannot guarantee that a correct energy function will be used when checking this box!

Bottom line: this check box was meant to cater to niche applications and should not be necessarily for routine usage; if you are not sure what to do, do not check it!

* Toppar stream file generated by
* CHARMM General Force Field (CGenFF) program version 2.2.0
* For use with CGenFF version 4.0
*

read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 2.2.0
* using valence-based bond orders
*
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 ligand_w       0.000 ! param penalty=   0.000 ; charge penalty=   0.000
GROUP            ! CHARGE   CH_PENALTY
ATOM C1     CG2R61 -0.115 !    0.000
ATOM C2     CG2R61 -0.115 !    0.000
ATOM C3     CG2R61 -0.115 !    0.000
ATOM C4     CG2R61 -0.115 !    0.000
ATOM C5     CG2R61 -0.115 !    0.000
ATOM C6     CG2R61 -0.115 !    0.000
ATOM H1     HGR61   0.115 !    0.000
ATOM H2     HGR61   0.115 !    0.000
ATOM H3     HGR61   0.115 !    0.000
ATOM H4     HGR61   0.115 !    0.000
ATOM H5     HGR61   0.115 !    0.000
ATOM H6     HGR61   0.115 !    0.000
               ! Bond order
BOND C1   C2   ! 2
BOND C1   C6   ! 1
BOND C1   H1   ! 1
BOND C2   C3   ! 1
BOND C2   H2   ! 1
BOND C3   C4   ! 2
BOND C3   H3   ! 1
BOND C4   C5   ! 1
BOND C4   H4   ! 1
BOND C5   C6   ! 2
BOND C5   H5   ! 1
BOND C6   H6   ! 1

END

read param card flex append
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 2.2.0
*

! 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
CG2R61 CG2R61  305.00     1.3750 ! PROT benzene, JES 8/25/89
CG2R61 HGR61   340.00     1.0800 ! PROT phe,tyr JES 8/25/89

ANGLES
CG2R61 CG2R61 CG2R61   40.00    120.00   35.00   2.41620 ! PROT JES 8/25/89
CG2R61 CG2R61 HGR61    30.00    120.00   22.00   2.15250 ! PROT JES 8/25/89 benzene

DIHEDRALS
CG2R61 CG2R61 CG2R61 CG2R61     3.1000  2   180.00 ! PROT JES 8/25/89
CG2R61 CG2R61 CG2R61 HGR61      4.2000  2   180.00 ! PROT JES 8/25/89 benzene
HGR61  CG2R61 CG2R61 HGR61      2.4000  2   180.00 ! PROT JES 8/25/89 benzene

IMPROPERS

END
RETURN

Se cancela este metodo, se prefiere el metodo mencionado en el post http://rtech.cl/cgenff-running-simulations-with-other-programs/

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