Re: [AMBER] xLEaP Na+ Cl-

From: Asaminew Haile <>
Date: Thu, 27 Nov 2014 07:05:42 -0500

Try this
loadamberparams frcmod.ionsjc_tip3p

> On Nov 27, 2014, at 7:01 AM, Weinzierl, Robert O J <> wrote:
> Dear Amber Users,
> I just installed AmberTools and Amber 14. The programs installed correctly and seems to work correctly (just one possible failure).
> After launching xLEaP in the usual manner with ff14SB ($AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB), I neutralized my structure (addions foo Na+ 0) and solvated it in a TIP3P solvent box. I encountered problems when I tried to create the prmtop and inpcrd files, because the Na+ ions could not be found ("For atom .R<Na+ 4> .A<Na+ 1> : could not find vdW (or other parameters for type Na+").
> After listing the loaded parameters I saw "NA" listed (as well as CL, Cl-, K, etc.), so I repeated the addions command (addions foo NA 0), but encountered the same problem when trying to save the prmtop and inpcrd files. CL/Cl- ions were not recognized either.
> Any suggestions?
> Dr. Robert O.J. Weinzierl,
> Imperial College London
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Received on Thu Nov 27 2014 - 04:30:03 PST
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