[AMBER] For atom: .R<Na+ 127>.A<Na+ 1> Could not find type: Na+

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 24 Apr 2012 19:59:01 +0200

I'm trying to create topology files for a constant pH simulation of a protein ligand complex.

I've loaded: tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.constph

I tried to neutralise the system by: addions COMPLEX Na+ 0 (5 ions added).

When I tried to save the topology and coordinate files I've got "For atom: .R<Na+ 127>.A<Na+ 1> Could not find type: Na+"

I checked the archive and found that the problem had been reported earlier (25 July 2010). The suggestion by Bill Ross was to find a load an appropriate "parm.dat (or frcmod)
having the parameters for Na+ vdw". It was suggested that such file may be " in /amber10/dat/leap/parm/ since we see /amber10/dat/leap/parm/parm10.dat (or possibly in /amber10/dat/leap/lib/). With that in mind you might see a .dat or .frcmod file with a name including 'ion' - grep Na+ to determine if it is there and try loading that".

One such file is frcmod.ionsjc_spce. I'm not sure if this is the right one for the purpose of my simulation.

I tried to load it by: tleap -s -f $AMBERHOME/dat/leap/parm/frcmod.ionsjc_spce

and got: syntax error.

Any help on how to get round this problem is much appreciated



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Received on Tue Apr 24 2012 - 11:00:02 PDT
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