Open the receptor in Maestro or MMV and prepare the receptor to correct
bond order torsion terms extra. Trim hydrogens from the receptor as leap
will automatically add those.
The main problem is there is cystine residue in those terms. What you have
to do is rename CYS to CYX and then amber will feel that. CYS has bond like
mentioned ijn the error message but CYX will have something like CT-S. Edit
the PDB file using text editor word-pad to substitute. Rerun the PDB all
will be good.
I dont know if you have protein preparation wizard or not but using PPP of
Schrodinger you can fix all these errors very smoothly.
Best!!
SB
On Wed, Jul 2, 2014 at 9:07 AM, Harmeet Kaur <meet.academia.gmail.com>
wrote:
> ---------- Forwarded message ----------
> From: Harmeet Kaur <meet.academia.gmail.com>
> Date: Wed, Jul 2, 2014 at 12:05 PM
> Subject: error: unable to generate parameter file
> To: amber.ambermd.org
>
>
> Hi
>
> I have encountered the following error while running tleap on the structure
> with PDB Id 1A2Y. Kindly suggest how to overcome this error.Thanks in
> advance
>
>
> 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
> 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
> 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
> ** 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 1135 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
>
>
> --
> Regards
> Harmeet Kaur
> PhD Research Scholar
> UNESCO Regional Centre for Biotechnology
> 180 Udyog Vihar Phase 1
> Gurgaon-122016, India.
> Phone: +91-0124-2848800
>
>
>
> --
> Regards
> Harmeet Kaur
> PhD Research Scholar
> UNESCO Regional Centre for Biotechnology
> 180 Udyog Vihar Phase 1
> Gurgaon-122016, India.
> Phone: +91-0124-2848800
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Wed Jul 02 2014 - 00:30:02 PDT
