[AMBER] -Antechamber error for modified residues

From: Patil Pranita Uttamrao <bo19resch01001.iith.ac.in>
Date: Thu, 26 Sep 2019 11:46:49 +0530

Dear all,
I am trying to prepare the residue library and force field parameters of
the modified residue G7M(.cif attached) using antechamber as given below.

$ antechamber -fi ccif -i G7M.cif -bk G7M -fo ac -o G7M.ac -c bcc -at amber

but i am getting error as below

Info: Bond types are assigned for valence state (3) with penalty (1).

Info: Total number of electrons: 195; net charge: 1

Info: The number of electrons is odd (195).

      Please check the total charge (-nc flag) and spin multiplicity (-m
flag).

Running: AmberTools/amber18/bin/sqm -O -i sqm.in -o sqm.out

/AmberTools/amber18/bin/to_be_dispatched/antechamber: Fatal Error!

Cannot properly run "/home/pranita/AmberTools/amber18/bin/sqm -O -i sqm.in
-o sqm.out".

i tried with adding -nc -1 but still i am getting the exact same error
message.


so just to be sure i tried with mol2 file (pdb to mol2 )of this residue

antechamber -fi mol2 -i g7m.mol2 -nc -1 -bk G7M -fo ac -o g7m.ac -c bcc

its creating the .ac file without any error

Info: Bond types are assigned for valence state (5) with penalty (1).
Info: Total number of electrons: 198; net charge: -1

then using prepgen and parmchk2 i prepared frcmod.g7m, frcmod1.g7m and
frcmod2.g7m but the files don't seem right .

so i will be grateful if you can help with this.


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Received on Wed Sep 25 2019 - 23:30:01 PDT
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