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From: Aditya Setiajid <setiajid11.yahoo.com>

Date: Mon, 2 Apr 2012 14:33:08 +0800 (SGT)

Dear Amber Users,

I tried to made a prmtop and inpcrd file using antechamber for protein ligand complex. I used 6COX from pdb for the protein, and i have truncated the protein into one chain (chain A and S58 only, it means i also cut the nag and hem residue)

when i used command :

saveamberparm [file] [file].prmtop [file].inpcrd

the report is:

FATAL: Atom .R<ASN 582>.A<C 3> does not have a type.

FATAL: Atom .R<ASN 582>.A<O 4> does not have a type.

FATAL: Atom .R<ASN 582>.A<CB 5> does not have a type.

FATAL: Atom .R<ASN 582>.A<CG 6> does not have a type.

FATAL: Atom .R<ASN 582>.A<OD1 7> does not have a type.

FATAL: Atom .R<ASN 582>.A<ND2 8> does not have a type.

FATAL: Atom .R<VAL 583>.A<N 1> does not have a type.

FATAL: Atom .R<VAL 583>.A<CA 2> does not have a type.

FATAL: Atom .R<VAL 583>.A<C 3> does not have a type.

FATAL: Atom .R<VAL 583>.A<O 4> does not have a type.

FATAL: Atom .R<VAL 583>.A<CB 5> does not have a type.

FATAL: Atom .R<VAL 583>.A<CG1 6> does not have a type.

FATAL: Atom .R<VAL 583>.A<CG2 7> does not have a type.

FATAL: Atom .R<GLN 584>.A<N 1> does not have a type.

FATAL: Atom .R<GLN 584>.A<CA 2> does not have a type.

FATAL: Atom .R<GLN 584>.A<C 3> does not have a type.

FATAL: Atom .R<GLN 584>.A<O 4> does not have a type.

FATAL: Atom .R<GLN 584>.A<CB 5> does not have a type.

FATAL: Atom .R<GLN 584>.A<CG 6> does not have a type.

FATAL: Atom .R<GLN 584>.A<CD 7> does not have a type.

FATAL: Atom .R<GLN 584>.A<OE1 8> does not have a type.

FATAL: Atom .R<GLN 584>.A<NE2 9> does not have a type.

please help me

Best Regards,

Muhammad Aditya

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Received on Mon Apr 02 2012 - 00:00:03 PDT

Date: Mon, 2 Apr 2012 14:33:08 +0800 (SGT)

Dear Amber Users,

I tried to made a prmtop and inpcrd file using antechamber for protein ligand complex. I used 6COX from pdb for the protein, and i have truncated the protein into one chain (chain A and S58 only, it means i also cut the nag and hem residue)

when i used command :

saveamberparm [file] [file].prmtop [file].inpcrd

the report is:

FATAL: Atom .R<ASN 582>.A<C 3> does not have a type.

FATAL: Atom .R<ASN 582>.A<O 4> does not have a type.

FATAL: Atom .R<ASN 582>.A<CB 5> does not have a type.

FATAL: Atom .R<ASN 582>.A<CG 6> does not have a type.

FATAL: Atom .R<ASN 582>.A<OD1 7> does not have a type.

FATAL: Atom .R<ASN 582>.A<ND2 8> does not have a type.

FATAL: Atom .R<VAL 583>.A<N 1> does not have a type.

FATAL: Atom .R<VAL 583>.A<CA 2> does not have a type.

FATAL: Atom .R<VAL 583>.A<C 3> does not have a type.

FATAL: Atom .R<VAL 583>.A<O 4> does not have a type.

FATAL: Atom .R<VAL 583>.A<CB 5> does not have a type.

FATAL: Atom .R<VAL 583>.A<CG1 6> does not have a type.

FATAL: Atom .R<VAL 583>.A<CG2 7> does not have a type.

FATAL: Atom .R<GLN 584>.A<N 1> does not have a type.

FATAL: Atom .R<GLN 584>.A<CA 2> does not have a type.

FATAL: Atom .R<GLN 584>.A<C 3> does not have a type.

FATAL: Atom .R<GLN 584>.A<O 4> does not have a type.

FATAL: Atom .R<GLN 584>.A<CB 5> does not have a type.

FATAL: Atom .R<GLN 584>.A<CG 6> does not have a type.

FATAL: Atom .R<GLN 584>.A<CD 7> does not have a type.

FATAL: Atom .R<GLN 584>.A<OE1 8> does not have a type.

FATAL: Atom .R<GLN 584>.A<NE2 9> does not have a type.

please help me

Best Regards,

Muhammad Aditya

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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Received on Mon Apr 02 2012 - 00:00:03 PDT

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