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

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 2 Apr 2012 23:41:35 -0400

Those messages sound like you have disulfide bonds defined in the connect records of your pdb file, but that you never changed the residue name of the cysteines involved in the cystine bond from CYS to CYX in the pdb file.

Try doing that.

Hth,
Jason 

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Apr 2, 2012, at 10:32 PM, Aditya Setiajid <setiajid11.yahoo.com> wrote:
> 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
> <6COXS.pdb>
> <log_tleap.txt.txt>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Apr 02 2012 - 21:00:03 PDT
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