Hi,
Today, i repeat my job from beginning.. but now the error message was different from yesterday.. here is my step:
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, this message appeared:
Checking Unit.
WARNING: The unperturbed charge of the unit: -3.001000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Building angle parameters.
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Building proper torsion parameters.
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
Building improper torsion parameters.
total 1866 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
could anyone have any idea for this error message? here i attached my pdb file and my log file.
Best Regards,
Muhammad Aditya
________________________________
From: "steinbrt.rci.rutgers.edu" <steinbrt.rci.rutgers.edu>
To: Aditya Setiajid <setiajid11.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, April 2, 2012 8:50 PM
Subject: Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex
Hi,
>> FATAL: Atom .R<ASN 582>.A<C 3> does not have a type.
ASN is a standard residue and leap seems to have digested the previous 581
residues fine, so this sounds like your pdb file contains some atom names
not recognized by leap. Check the pdb file if atom 'C' in residue 582 is
somehow different, e.g. the atom naming scheme compared to other ASNs,
indentation, duplicate atoms, misplaced TER within the residue, last atom
in the pdb, etc...
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/x-palm-database attachment: 6COXS.pdb
Received on Mon Apr 02 2012 - 20:00:04 PDT
