[gmx-users] ionic charge

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 20 16:08:25 CEST 2006

Giacomo Bastianelli wrote:
> Where do I found the information regarding the
> overall charge of my protein (to counteract...)?

Run grompp and it will tell you. Read the output closely and pay 
attention to the warnings and errors it gives.

gromacs is really quite good at giving useful feedback about possible 
and actual problems. It must be a little vexing to those who put such 
time and care into making gromacs give that feedback that (for example) 
you've used a command line with two -c options, and got an explicit 
error message that told you that, and you needed to ask the mailing list 
what the problem was, and didn't have the courtesy to quote us the 
command line you used so we'd actually have the information we might 
have needed to help you :-) I realise you're new, but if you want free 
help from busy knowledgeable people, you need to try hard to make it 
easy for them to help you, and to demonstrate that you're actively 
trying to solve your own problems :-)

Happy MDing!


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