Hi dear all.
I am trying to create prmtop and inpcrd files for ADP and ATP, I downloaded
my structure from pdb.org (13PK) in sdf format. I converted it with
Avogadro to pdb format and tried to obtain its parameters with RED_tools,
but the optimization geometry failed. I tried to used RED-server but it
only gave me a mol.p2n file.
Then, I tried to convert sdf to mol2 format with Avogadro, but when I
loaded ado.mol2 file I put check adp and sent me the next message:
Could not find angle parameter: N.ar - C.ar - N.ar
Could not find angle parameter: N.ar - C.ar - C.ar
Could not find angle parameter: N.ar - C.ar - N.ar
Could not find angle parameter: C.ar - N.ar - C.ar
Could not find angle parameter: C.ar - N.ar - C.ar
Could not find angle parameter: N.ar - C.ar - C.ar
Could not find angle parameter: N.ar - C.ar - C.ar
Could not find angle parameter: C.ar - C.ar - N.pl3
Could not find angle parameter: C.ar - C.ar - N.ar
Could not find angle parameter: C.ar - C.ar - N.ar
Could not find angle parameter: C.ar - C.ar - C.ar
Could not find angle parameter: C.ar - N.ar - C.ar
Could not find angle parameter: N.pl3 - C.ar - N.ar
Could not find angle parameter: N.ar - C.ar - N.ar
Could not find angle parameter: C.ar - N.ar - C.ar
There are missing parameters.
check: Warnings: 1
Unit is OK.
Therefore I downloaded from
http://www.pharmacy.manchester.ac.uk/bryce/amber/ the frcmod.phos file
which contains parameters for ADP and I got the same message.
Does anyone could help me?
Thanks in advance
Regards
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Received on Wed May 13 2015 - 09:00:04 PDT
