AMBER Archive (2006)

Subject: AMBER: saveamberparams error in Amber9

From: Weihua Li (whli.ecust_at_gmail.com)
Date: Wed Jun 14 2006 - 08:28:43 CDT

Dear all,
        Program: xleap/tleap in Amber9
        Protein: a protein containing HEME
        I are using xleap/tleap to prepare the protein.top, but the error
messages are given as enclosed. Surprisingly, I did not get the errors
when using Amber8 with the same commands.
        The hem.in and hem.frcmod files are taken from
$AMBERHOME/dat/contrib/heme. The atom types, such as NP, NO ,and CX, are
indeed included in the MASS section in the hem.frcmod.
        Could anybody with experience give me some advice?

        The commands I used in xleap are as follows:
> xleap -s -f leaprc.ff03
> loadamberprep hem.in
>loadamberparams hem.frcmod
>p=loadpdb protein.pdb
>saveamberparm p p.top 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. 

-- 
Best regards,
Weihua

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