Hi,
I am trying to make a subset of fragments of the molecule hexanol from an
amber library file.
I created the library file using RED III and gaussian.
if the backbone of hexanol is O1-C1-C2-C3-C4-C5-C6
I would like to create a series of parm files that are fragments of this.
e.g.
C1-C2
C2-C3
C3-C4
C4-C5
C5-C6
(note the above fragments also include their associated hydrogens)
To try and do this, I have used tleap and run the following commands:
tleap
####
source leaprc.gaff
loadoff hexanol_final.lib
remove hex.hex hex.hex.1
remove hex.hex hex.hex.2
remove hex.hex hex.hex.9
remove hex.hex hex.hex.10
remove hex.hex hex.hex.11
remove hex.hex hex.hex.12
remove hex.hex hex.hex.13
remove hex.hex hex.hex.14
remove hex.hex hex.hex.15
remove hex.hex hex.hex.16
remove hex.hex hex.hex.17
remove hex.hex hex.hex.18
remove hex.hex hex.hex.19
remove hex.hex hex.hex.20
remove hex.hex hex.hex.21
saveamberparm hex CT1_CT2.parm CT1_CT2.crd
###
However, I get an error saying:
saveAmberParm: There are no parameter sets loaded
I have also tried creating a new library file (e.g. CT1_CT2.lib), loading it
in and trying saveamberparm. However, I get the same error
I chose tleap to do this vs xleap, as there a lot of fragments and I need to
be able to script this. Obviously, I am not understanding something
fundamental in the way amber saves the parameter files, so I was hoping
someone might be able to point me in the right direction.
Best regards,
GT
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Received on Mon Jul 25 2011 - 20:00:03 PDT
