Dear Amber users,
I was trying to prepare the required parameter files to run a simulation
task for my protein, everything worked well with antechamber and parmchk..
But when I try to save .prmtop and .prmcrd files, it gives following error..
saveamberparm x andy-new.prmtop andy-new.prmcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: O2 - ca
Building angle parameters.
Could not find angle parameter: O2 - ca - ca
Could not find angle parameter: O2 - ca - ha
Could not find angle parameter: O2 - ca - ca
Could not find angle parameter: C - O2 - ca
Building proper torsion parameters.
** No torsion terms for O2-C-O2-ca
** No torsion terms for C-O2-ca-ca
** No torsion terms for C-O2-ca-ha
** No torsion terms for C-O2-ca-ca
** No torsion terms for CT-C-O2-ca
Building improper torsion parameters.
old PREP-specified impropers:
<IXX 604>: C12 C10 C11 N1
<IXX 604>: C11 C9 C10 H10
<IXX 604>: C10 C8 C9 H9
<IXX 604>: C7 C9 C8 H8
<IXX 604>: C12 C8 C7 H7
<IXX 604>: C6 C7 C12 C11
<IXX 604>: C5 C4 C13 C14
<IXX 604>: C13 C3 C4 H4
<IXX 604>: C4 C2 C3 H3
<IXX 604>: C3 C1 C2 H2
<IXX 604>: C2 C14 C1 H1
<IXX 604>: C13 C1 C14 N1
<IXX 604>: C15 C14 N1 C11
total 1802 improper torsions applied
13 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
I fould similar post in the archieves (
http://archive.ambermd.org/200605/0141.html), but it is related to calcium
and not with C-alpha, I guess.
Looking forward for your valuable consideration and suggestions.
Thanking you,
Yogesh
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Received on Tue Jul 14 2009 - 10:09:28 PDT
