VMD-L Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Jul 10 2019 - 09:49:09 CDT

Dear Yang,

 

If you open the protein parameters file from CHARMM36, you will see that the water is not defined there. You need to add “parameters toppar_water_ions.str” to your NAMD configuration file. This is valid for the water and ions.

 

Best

 

João

 

 

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of 黄洋 <leolovege_at_stu.xmu.edu.cn>
Date: Wednesday, July 10, 2019 at 9:04 AM
To: <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT

 

Dear Sir:

I used to use all27 as the force field parameter, but I got an error when I changed it to all36.

Errors:

FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT

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I have used top_all27_prot_lipid_na.inp as topology file to build .psf file by VMD Autopsf module. futhermore, I carried out molecular dynamics simulation using par_all27_prot_lipid.inp as force field parameters in NAMD.

It always works until topology file was replaced with top_all36_prot.rtf and force field parameters file was replaced with par_all36_prot.prm.

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I would be appreciated if anyone could tell me how to solve it.

Thanks

 

Yang Huang

Xiamen University.