Apologies if this was answered already. It looks like you didn’t neutralize and the "addions mol Cl- 0" command didn’t work for some reason. Go back and look at your leap.log file.
Maria
> On Oct 22, 2021, at 5:58 PM, Saikat Pal <saikatpaliitg.yahoo.com> wrote:
>
> 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
> quit
>
> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 26 2021 - 17:30:02 PDT
