AMBER Archive (2007)

Subject: Re: AMBER: not getting topology and restraint file

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jul 24 2007 - 09:46:49 CDT

could you show your leap input?

On 7/24/07, Prem Prakash Pathak <prempolymer_at_gmail.com> wrote:
> Hi
> I am runing the tleap
> but at the end i get following message
> Added missing heavy atom: .R<CTRP 191>.A<OXT 25>
> total atoms in file: 2681
> Leap added 226 missing atoms according to residue templates:
> 1 Heavy
> 225 H / lone pairs
> Total unperturbed charge: 6.000000
> Total perturbed charge: 6.000000
> ERROR: syntax error
>
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 6.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 581 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CTRP 1
> NMET 1
> )
> (no restraints)
> Quit
> struct_calc/amber>
>
> and finaly i am not getting the topology file and the restraint file
>
> what could be the problem
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