Dear amber users,
I have one problem in leap. When I load a pdb file of a protein into tleap
with ff99SB, and check it, there are some missing parameters like these:
Could not find bond parameter for: CT - O
Could not find bond parameter for: CT - O
Could not find bond parameter for: CT - O
Could not find bond parameter for: CT - O
Could not find bond parameter for: CT - O
Checking for angle parameters.
Could not find angle parameter: C - N - C
Could not find angle parameter: CT - CT - O
Could not find angle parameter: HC - CT - O
Could not find angle parameter: HC - CT - O
Could not find angle parameter: HC - CT - O
Could not find angle parameter: CT - O - C
Could not find angle parameter: CT - CT - O
Could not find angle parameter: CT - CT - O
Could not find angle parameter: HC - CT - O
Could not find angle parameter: HC - CT - O
Could not find angle parameter: CT - CX - CT
Could not find angle parameter: CT - O - C
Could not find angle parameter: CT - O - CT
Could not find angle parameter: CX - CT - O
Could not find angle parameter: N3 - CT - CX
Could not find angle parameter: N3 - CT - HC
Could not find angle parameter: N3 - CT - HC
Could not find angle parameter: N3 - CT - O
Could not find angle parameter: HC - CT - O
Could not find angle parameter: HC - CT - O
Could not find angle parameter: HC - CT - O
Could not find angle parameter: CT - O - C
Could not find angle parameter: CX - CT - O
Could not find angle parameter: CX - N - CX
Could not find angle parameter: N - CX - N
Could not find angle parameter: N - C - N
Could not find angle parameter: H1 - CT - O
Could not find angle parameter: H1 - CT - O
Could not find angle parameter: H1 - CT - O
Could not find angle parameter: CT - O - C
Could not find angle parameter: S - CT - O
Could not find angle parameter: S - CT - O
Could not find angle parameter: CT - CT - O
Could not find angle parameter: HC - CT - O
Could not find angle parameter: HC - CT - S
Could not find angle parameter: HC - CT - O
Could not find angle parameter: HC - CT - S
Could not find angle parameter: CT - O - C
Could not find angle parameter: CT - O - CT
Could not find angle parameter: CX - CT - O
There are missing parameters.
The attached file is that file rec1.pdb which is saved from another pdb
file (we may call rec.pdb) after some manipulations (only matchmaker,
deleting hydrgens) in Chimera. It is ok for rec.pdb to load into tleap, but
for rec1.pdb, it is not. I don't know how to explain it. Could some help me
to figure it out so that I can avoid it next time? Thanks so much.
--
Best Regards,
Qinghua
Ph.D. student
Juelich Research Center
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Received on Wed Nov 16 2011 - 01:30:03 PST
