Dear all,
I tried to generate the topology of non-standard amino acid residues using antechamber following the tutorial
http://ambermd.org/antechamber/pro4.html
4-Hydroxyl-Proline (PR4) - AMBER<
http://ambermd.org/antechamber/pro4.html>
ambermd.org
4-Hydroxyl-Proline (PR4) Step 1: Prepare two mol2 files: alpha and beta conformatons for ACE-PR4-ACE (Take a look at the molecular structure ) Step 2: Generate two gaussian input files: alpha and beta using the following antechamber command: antechamber -fi mol2 -fo gzmat -i pro4a.mol2 -o pro4a.gau
However, the following steps,
loadamberprep pro4.prepi
loadamberparams pro4.frcmod
aa =sequence {ALA PR4 ALA}
saveamberparm aa ala-pr4-ala.prmtop ala-pr4-ala.prmcrd
gives the following error,
Error: Could not find bond parameter for: C - n
Error: Could not find bond parameter for: c - N
Building angle parameters.
Error: Could not find angle parameter: O - C - n
Error: Could not find angle parameter: C - n - c3
Error: Could not find angle parameter: C - n - c3
Error: Could not find angle parameter: CX - C - n
Error: Could not find angle parameter: o - c - N
Error: Could not find angle parameter: c - N - H
Error: Could not find angle parameter: c - N - CX
Error: Could not find angle parameter: c3 - c - N
Building proper torsion parameters.
Error: ** No torsion terms for O-C-n-c3
Error: ** No torsion terms for O-C-n-c3
Error: ** No torsion terms for CX-C-n-c3
Error: ** No torsion terms for CX-C-n-c3
Error: ** No torsion terms for o-c-N-H
Error: ** No torsion terms for o-c-N-CX
Error: ** No torsion terms for c3-c-N-H
Error: ** No torsion terms for c3-c-N-CX
Building improper torsion parameters.
old PREP-specified impropers:
<PR4 2>: -M C3 N1 C2
<PR4 2>: +M C3 C9 O13
total 5 improper torsions applied
2 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Warning: Parameter file was not saved.
Please help. Thanks in advance.
Rituparna Roy,
Junior Research Fellow,
Department of Chemistry,
Indian Institute of Technology Guwahati.
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Received on Wed Feb 27 2019 - 07:00:02 PST
