Re: CHARMM-GUI running error for ligand

From: Chiara Cosenza unina (chiara.cosenza_at_unina.it)
Date: Fri Mar 30 2012 - 05:05:58 CDT

Hello Albert
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

On 03/30/2012 09:37 AM, Albert wrote:
> Hello:
> I've generated a system containing a ligand within it by CHARMM-GUI.
> and I am trying to run step6.1 keeping all parameters unmodified by
> command:
> namd2 +p8 step6.1_eq.inp >log &
>
> but it said from log file:
>
> Info: COORDINATE PDB ../step5_assembly.pdb
> Info: STRUCTURE FILE ../step5_assembly.xplor.psf
> Info: PARAMETER file: CHARMM format!
> Info: PARAMETERS toppar/par_all22_prot.prm
> Info: PARAMETERS toppar/par_all27_na.prm
> Info: PARAMETERS toppar/par_all36_carb.prm
> Info: PARAMETERS toppar/par_all36_lipid.prm
> Info: PARAMETERS toppar/par_all36_cgenff.prm
> Info: PARAMETERS toppar/toppar_water_ions.str
> Info: PARAMETERS toppar/toppar_all36_lipid_cholesterol.str
> Info: PARAMETERS toppar/lig.prm
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Info: SUMMARY OF PARAMETERS:
> Info: 1314 BONDS
> Info: 3871 ANGLES
> Info: 9238 DIHEDRAL
> Info: 274 IMPROPER
> Info: 6 CROSSTERM
> Info: 481 VDW
> Info: 6 VDW_PAIRS
> Info: 0 NBTHOLE_PAIRS
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG32
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG32
>
> Charm++ fatal error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG32
>
> does anybody have any idea how to solve this problem?
>
> THX
>
>

-- 
Chiara Cosenza
PhD student
University of Naples "Federico II"
IIT_at_CRIB - Center for Advanced Biomaterials for Healthcare
P.le Tecchio 80,80125
Naples-Italy
http://abcnapoli.iit.it/
email: chiara.cosenza_at_unina.it
email: chiara.cosenza_at_iit.it
m.      +39 3383459467

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