I want to perform 100 ns simulation for protein that contain two zinc-finger motifs using NAMD, but it turns out that I can´t find the topology and parameters files for the CYSD and CCCC patch. I have seen some that have been modified but I can´t run them cause of error mesages: Rason: FATAL ERROR: BAD vdw FORMAT IN CHARMM PARAMETER FILE
*INE= PRESS CYSD -1
If anyone could help 1i´ll very much appreciates.
Thanks to all for your attention!!
Hi Lilian,
The error you have got is because the format only. You can find the topology for CYS and also for zinc (ZN) in CHARMM force field.
I'd suggest you to submit your protein under Charmm-gui (http://www.charmm-gui.org/) to obtain the input parameters correctly. Follow each step carefully.
Please, be sure that you maintained the zinc ion in the system before to run it.
Best,
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