From: Albert (mailmd2011_at_gmail.com)
Date: Fri Mar 30 2012 - 05:27:35 CDT
Hi Chiara:
thank you very much for kind messages. but it is there in my psf file:
5141 HETA 1 LIG C22 CG32 -0.180000 12.0110 0
0.00000 -0.301140E-02
5142 HETA 1 LIG C19 CG32 -0.179000 12.0110
0 0.00000 -0.301140E-02
5143 HETA 1 LIG H24 HGA2 0.900000E-01 1.00800
0 0.00000 -0.301140E-02
5144 HETA 1 LIG H23 HGA2 0.900000E-01 1.00800
0 0.00000 -0.301140E-02
5145 HETA 1 LIG H21 HGA2 0.900000E-01 1.00800
0 0.00000 -0.301140E-02
5146 HETA 1 LIG H20 HGA2 0.900000E-01 1.00800
0 0.00000 -0.301140E-02
5147 HETA 1 LIG C16 CG32 -0.181000 12.0110
0 0.00000 -0.301140E-02
On 03/30/2012 12:05 PM, Chiara Cosenza unina wrote:
> 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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