[AMBER] Magnesium FATAL error

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Thu, 12 Jun 2014 01:46:00 -0700

Hi All;

It might be a repeating question. But I have one receptor with MG inside
it. Please check the file attached. I used FF13 force field to treat the
receptor but gives an error

FATAL: Atom .R<g 561>.A<MG 1> does not have a type.
FATAL: Atom .R<g 560>.A<MG 1> does not have a type.

Is there any bug fixes for that in any updates. Or is there any technique
so that we can amend something inside /home/smoonsamy/amber12/dat/leap/cmd

The last MG line inside the receptor looks like this

HETATM 4378 MG Mg 396 -36.722 30.668 -15.949 1.00 43.50
HETATM 4379 MG Mg 397 -36.397 34.266 -16.919 1.00 39.65

The tleap we used looks like this

source leaprc.ff13
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
receptor = loadPDB rec.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm LIG LIG.top LIG.crd
receptor = loadPDB rec.pdb
saveAmberParm receptor rec.top rec.crd
saveAmberParm complex com.top com.crd
savepdb complex complex_gas.pdb
charge complex
addIons2 complex Na+ 0
solvateBox complex TIP3PBOX 12.0
saveAmberParm complex com_solvated.top com_solvated.crd
savepdb complex com_solvated.pdb

Help will be highly appreciated.

Thanks & Regards;
Soumendranath Bhakat

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Received on Thu Jun 12 2014 - 02:00:03 PDT
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