AMBER Archive (2006)

Subject: Re: AMBER: saveamberparams error in Amber9

From: David A. Case (
Date: Wed Jun 14 2006 - 22:15:05 CDT

On Wed, Jun 14, 2006, Weihua Li wrote:

> The commands I used in xleap are as follows:
> > xleap -s -f leaprc.ff03
> > loadamberprep
> >loadamberparams hem.frcmod
> >p=loadpdb protein.pdb
> >saveamberparm p p.crd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 5.000000 is not zero.
> -- ignoring the warning.
> Building topology.
> Building atom parameters.
> For atom: .R<HEM 466>.A<NA 2> Could not find type: NP
> For atom: .R<HEM 466>.A<NB 23> Could not find type: NO
> For atom: .R<HEM 466>.A<CBB 32> Could not find type: CX
> For atom: .R<HEM 466>.A<NC 39> Could not find type: NP
> For atom: .R<HEM 466>.A<CBC 48> Could not find type: CX
> For atom: .R<HEM 466>.A<ND 55> Could not find type: NO
> Parameter file was not saved.

These heme parameters were developed long before ff03. Basically, parm94.dat
defines van der Waals parameters for NP, NO, CX, but parm99.dat (from which
ff03 was developed) does not. So, you will need to copy the van der Waals
parameters from parm94.dat into your frcmod file if you want to use ff03
as the rest of the force field.

Note that in parm94.dat, NP and NO are equivalenced to "N", and CX is
equivalenced to "C". So, you will either need to extend the equivalence list
in parm99.dat (simplest solution), or create the necessary vdW parameters in
your frcmod files.

...good luck....dac

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