[gmx-users] remove the atom clashes-reg

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 31 10:24:19 CEST 2011

On 31/08/2011 6:15 PM, ITHAYARAJA wrote:
> Hi Dear,
> I am doing simulation with three ligand so that I have applied 
> deprecated force field to the system.

That's a bad reason to choose a deprecated force field.

> I went through the reference which you cited to the following error. I 
> understood the error that It could be a clashes. It wanted to  remove 
> atom clashes from my coordinate file, so Is there any option to do the 
> same.

You need to design your coordinate file construction or system 
preparation protocol better. We can't help because we don't know what 
you're doing. Follow the links from the URL I gave last time. Read as 
much as you can. Describe as fully as you can when asking for help.

> help me.........
> Program grompp, VERSION 4.0.7
> Source code file: ../../../../src/kernel/toppush.c, line: 947
> Fatal error:
> Atomtype NR not found

Whatever you did to your topology had nothing to do with helping resolve 
atomic clashes.


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