Re: CHARMM-GUI running error for ligand

From: Albert (mailmd2011_at_gmail.com)
Date: Fri Mar 30 2012 - 05:48:12 CDT

Hi hannes:
  thank you very much for kind messages. It seems that there is no atom
type in the .prm file from CHARMM-GUI output. Do you have any
suggestions for solving this problem? I also generate several topology
file for ligands, and there are always some atom cannot file VDW
paramters.....

here is the output for .prm file from CHARMM-GUI

* 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
CG2D1 CG311 365.00 1.5020 ! Mol_ante , from CG2D1 CG321, penalty= 4

ANGLES
CG2D1 CG2D1 CG311 48.00 123.50 ! Mol_ante , from CG2D1 CG2D1
CG321, penalty= 0.6
CG311 CG2D1 HGA4 40.00 116.00 ! Mol_ante , from CG321 CG2D1
HGA4, penalty= 0.6
CG2D1 CG311 CG314 32.00 112.20 ! Mol_ante , from CG2D1 CG321
CG321, penalty= 21
CG2D1 CG311 OG311 75.70 110.10 ! Mol_ante , from CG2D1 CG321
OG311, penalty= 4
CG2D1 CG311 HGA1 45.00 111.50 ! Mol_ante , from CG2D1 CG321
HGA2, penalty= 4
CG314 CG311 OG311 75.70 112.10 ! Mol_ante , from CG324 CG311
OG311, penalty= 0.6
CG311 CG314 CG321 58.35 113.50 11.16 2.56100 ! Mol_ante ,
from CG321 CG314 CG321, penalty= 0.6
CG314 CG321 OG303 75.70 110.10 ! Mol_ante , from CG324 CG321
OG303, penalty= 0.6

DIHEDRALS
CG311 CG2D1 CG2D1 CG321 0.4500 1 180.00 ! Mol_ante , from
CG321 CG2D1 CG2D1 CG321, penalty= 0.6
CG311 CG2D1 CG2D1 CG321 8.5000 2 180.00 ! Mol_ante , from
CG321 CG2D1 CG2D1 CG321, penalty= 0.6
CG311 CG2D1 CG2D1 HGA4 1.0000 2 180.00 ! Mol_ante , from
CG321 CG2D1 CG2D1 HGA4, penalty= 0.6
CG2D1 CG2D1 CG311 CG314 0.6000 1 180.00 ! Mol_ante , from
CG2D1 CG2D1 CG321 CG321, penalty= 21
CG2D1 CG2D1 CG311 OG311 1.9000 1 180.00 ! Mol_ante , from
CG2D2 CG2D1 CG321 OG311, penalty= 7.5
CG2D1 CG2D1 CG311 OG311 0.4000 2 180.00 ! Mol_ante , from
CG2D2 CG2D1 CG321 OG311, penalty= 7.5
CG2D1 CG2D1 CG311 OG311 0.6000 3 180.00 ! Mol_ante , from
CG2D2 CG2D1 CG321 OG311, penalty= 7.5
CG2D1 CG2D1 CG311 HGA1 0.3000 3 180.00 ! Mol_ante , from
CG2D1 CG2D1 CG321 HGA2, penalty= 4
HGA4 CG2D1 CG311 CG314 0.1200 3 0.00 ! Mol_ante , from
HGA4 CG2D1 CG321 CG321, penalty= 21
HGA4 CG2D1 CG311 OG311 0.2000 3 0.00 ! Mol_ante , from
HGA4 CG2D1 CG321 OG311, penalty= 4
HGA4 CG2D1 CG311 HGA1 0.0000 3 0.00 ! Mol_ante , from
HGA4 CG2D1 CG321 HGA2, penalty= 4
CG2D1 CG311 CG314 CG321 0.2000 3 0.00 ! Mol_ante , from
CG321 CG311 CG321 CG2D1, penalty= 5
CG2D1 CG311 CG314 NG3P3 0.2000 3 0.00 ! Mol_ante , from
NG3P3 CG314 CG321 CG2R61, penalty= 25
CG2D1 CG311 CG314 HGA1 0.2000 3 0.00 ! Mol_ante , from
HGA1 CG311 CG321 CG2D1, penalty= 5
OG311 CG311 CG314 CG321 0.1400 3 0.00 ! Mol_ante , from
CG311 CG311 CG311 OG311, penalty= 1.6
OG311 CG311 CG314 NG3P3 0.2000 3 0.00 ! Mol_ante , from
NG3P3 CG314 CG321 OG311, penalty= 4
OG311 CG311 CG314 HGA1 0.1950 3 0.00 ! Mol_ante , from
OG311 CG311 CG311 HGA1, penalty= 1
HGA1 CG311 CG314 CG321 0.1950 3 0.00 ! Mol_ante , from
CG321 CG311 CG311 HGA1, penalty= 1
CG2D1 CG311 OG311 HGP1 1.3000 1 0.00 ! Mol_ante , from
CG2D1 CG321 OG311 HGP1, penalty= 4
CG2D1 CG311 OG311 HGP1 0.7000 2 0.00 ! Mol_ante , from
CG2D1 CG321 OG311 HGP1, penalty= 4
CG2D1 CG311 OG311 HGP1 0.5000 3 0.00 ! Mol_ante , from
CG2D1 CG321 OG311 HGP1, penalty= 4
CG314 CG311 OG311 HGP1 0.5000 1 0.00 ! Mol_ante , from
CG324 CG311 OG311 HGP1, penalty= 0.6
CG314 CG311 OG311 HGP1 0.7000 2 0.00 ! Mol_ante , from
CG324 CG311 OG311 HGP1, penalty= 0.6
CG311 CG314 CG321 OG303 0.2000 3 180.00 ! Mol_ante , from
CG321 CG311 CG321 OG303, penalty= 1.6
CG311 CG314 CG321 HGA2 0.1950 3 0.00 ! Mol_ante , from
CG321 CG314 CG321 HGA2, penalty= 0.6
NG3P3 CG314 CG321 OG303 0.7000 1 180.00 ! Mol_ante , from
OG303 CG321 CG324 NG3P3, penalty= 4
HGA1 CG314 CG321 OG303 0.1950 3 0.00 ! Mol_ante , from
HGA1 CG311 CG321 OG303, penalty= 1
CG314 CG321 OG303 PG1 0.6000 1 180.00 ! Mol_ante , from
CG324 CG321 OG303 PG1, penalty= 0.6
CG314 CG321 OG303 PG1 0.6500 2 0.00 ! Mol_ante , from
CG324 CG321 OG303 PG1, penalty= 0.6
CG314 CG321 OG303 PG1 0.0500 3 0.00 ! Mol_ante , from
CG324 CG321 OG303 PG1, penalty= 0.6

IMPROPERS

END

On 03/30/2012 12:35 PM, Hannes Loeffler wrote:
>> Hi Chiara:
>> thank you very much for kind messages. but it is there in my psf
>> file:
>>> I think you have to check if thevdw parameter for ATOM TYPE CG32 is
>>> set in one of you parameters files. Maybe there's no correspondence
>>> between the name of atom type in psf and in the parameter files.
>>> Regards,
>>> Chiara
> The actual vdW parameters would be in the _parameter_ file as pointed
> out (not the PSF file). So check those. Probably it should be in
> toppar/lig.prm.

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