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 <case.biomaps.rutgers.edu>
To: Aditya Setiajid <setiajid11.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
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?
....dac
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Received on Mon Apr 02 2012 - 07:00:04 PDT
