Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex

From: Aditya Setiajid <>
Date: Mon, 2 Apr 2012 21:39:35 +0800 (SGT)

sorry for the incomplete explanation, i have already made the ligand prmtop and inpcrd before.. after that, when i want to make a ligand-protein complex prmtop and inpcrd, i meant that i used that command in tleap, here the commands that i give to tleap:

in order to get into tleap, i used this command:
tleap -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB

in leap, i used this commands:

1. source leaprc.gaff
2. loadamberparams [file].frcmod
3. loadoff [file].lib
4. complex = loadpdb [file].pdb

5. saveamberparm complex [file].prmtop [file].inpcrd
after this command (no.5) the fatal error messages appeared..  what's wrong with my job?

Best Regards,
Muhammad Aditya

 From: David A Case <>
To: Aditya Setiajid <>; AMBER Mailing List <>
Sent: Monday, April 2, 2012 7:08 PM
Subject: Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex
On Mon, Apr 02, 2012, Aditya Setiajid wrote:
> 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.

Please tell us the complete set of leap commands you used.  Did you load a
leaprc file?  Which one?  What other commands did you give to leap?  What
does antechamber have to do with this?

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Received on Mon Apr 02 2012 - 07:00:04 PDT
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