VMD-L Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Dec 16 2019 - 09:26:08 CST

Dear Mubarak,

 

Thank you for reporting. Does your newly parameterize molecule share the residue name with an already existing residue in the CHARMM force field? And did you select the option to print all the parameters in the str file when you submitted your molecule to the CGenFF website?

 

These are two significant sources of missing parameters when using QwikMD and CGenFF to prepare simulations.

 

Best,

 

João

 

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Mubarak Alamri <mubalamri_at_gmail.com>
Date: Saturday, December 14, 2019 at 6:31 PM
To: <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Charm++ fatal error: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 NG301 (ATOMS 6407 6408) .. ERROR) Error connecting to localhost on port 3000

 

Hi

I am trying to run MD simulation for ligand-protein complex using QwikMD.

I parametrize the ligand using https://cgenff.umaryland.edu/ following the protocol

However, I got this error message after running the simulation:

 

 

Charm++ fatal error:

 

 FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 NG301 (ATOMS 6407 6408)

 

 ERROR) Error connecting to localhost on port 3000

 

I open the port 3000 on my win10 and that did not help.

 

I attached the error .log file as well as a screenshot from VMD command window.

 

Thank you in advance I appreciate your help

 

M. Alamri