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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Received on Sun Jun 18 2006 - 06:07:07 PDT
