Dear Amber Users
I am trying to simulate cyclosporin in water. For the N-methylated
residues, I am using the FF_NCAA files. For the Bmt residue, I am trying to
generate the forcefield parameters using GAFF, following this tutorial at
https://ambermd.org/tutorials/basic/tutorial4b/
However, I am getting the following error:
/antechamber: Fatal Error!
Cannot properly run /bin/sqm -O -i sqm.in -o sqm.out".
The sqm.out file gives:
QMMM: System specified with odd number of electrons ( 57)
QMMM: but odd spin ( 1). You most likely have
the charge of QMMM: QM region
(qmcharge) set incorrectly. Correct error and re-run calculation.
Can someone please help me understand and rectify this?
Or if anyone has a parameter file for Bmt that they may have used earlier,
I'll be really obliged.
Also, when I am trying to run leap with the structure, I am using the
following in the leap.in file:
source leaprc.protein.ff14SB
source leaprc.gaff
loadAmberPrep ../ncaa_ff/ffncaa.in
mod1=loadAmberParams ../ncaa_ff/MLE.frcmod
mod2=loadAmberParams ../ncaa_ff/MVA.frcmod
mod3=loadAmberParams ../ncaa_ff/NMG.frcmod
mod4=loadAmberParams ../ncaa_ff/ABA.frcmod
seq = { ALA MLE MLE MVA BMT ABA NMG MLE VAL MLE ALA }
cycpep = loadPDBusingseq backbone.pdb seq
bond cycpep.1.N
cycpep.11.C
savepdb cycpep cyclosporin_out.pdb
saveAmberParm cycpep csp.top csp.crd
quit
There seems to be an error with the bond command:
bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
Can someone please help me identify where I am going wrong here?
Thanks a lot
Suchetana
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Received on Wed Oct 05 2022 - 13:30:03 PDT
