[AMBER] Query regarding ZAFF Modeling Tutorial

From: Saikat Pal <saikatpaliitg.yahoo.com>
Date: Fri, 22 Oct 2021 21:58:03 +0000 (UTC)

Dear all,
I am following the ZAFF Modeling Tutorial (https://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm). However, using the following command (which is in tutorial):

source leaprc.protein.ff14SB
addAtomTypes { { "ZN"  "Zn" "sp3" } { "S3"  "S" "sp3" } { "N2"  "N" "sp3" } }
loadoff atomic_ions.lib
source leaprc.water.tip3p
loadamberparams frcmod.ions1lm_126_tip3p
loadamberprep ZAFF.prep
loadamberparams ZAFF.frcmod
mol = loadpdb 2GIV_ZAFF.pdb
bond mol.98.ZN mol.34.SG
bond mol.98.ZN mol.37.SG
bond mol.98.ZN mol.50.NE2
bond mol.98.ZN mol.54.SG
charge mol
savepdb mol 2GIV_ZAFF_dry.pdb
saveamberparm mol 2GIV_ZAFF_dry.prmtop 2GIV_ZAFF_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Cl- 0
savepdb mol 2GIV_ZAFF_solv.pdb
saveamberparm mol 2GIV_ZAFF_solv.prmtop 2GIV_ZAFF_solv.inpcrd

I am getting the following warning :
/home/sp1564/.conda/envs/AmberTools21/bin/teLeap: Warning!
The unperturbed charge of the unit (1.000020) is not zero.

Thanks and Regards,
Saikat Pal

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Received on Fri Oct 22 2021 - 15:00:02 PDT
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