Hi All,
I am trying to generate parameters of modified residue. But I don't know how to start.
I tried this tutorial: Amber Basic Tutorials - Tutorial A26
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Amber Basic Tutorials - Tutorial A26
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I got an error. I changed lines following Amber mailing list and it worked.
But it didn't work with my system.
Here is the antechamber command:antechamber -fi pdb -i HAR.pdb -fo mol2 -o HAR.mol2 -c bcc -nc 0 -at amber -s 2 -dr no
And output:Welcome to antechamber 19.0: molecular input file processor.
Running: /amber18/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f acWarning: For atom (ID: 12, Name: OH1) the best APS is not zero. Bonds involving this atom are frozen.The frozen atom type can only be 1, 2, 3, 7 (aromatic single),or 8 (aromatic double)./amber18/bin/to_be_dispatched/antechamber: Fatal Error!Cannot properly run "/amber18/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac".
If I add -j flag, even then no luck!
Welcome to antechamber 19.0: molecular input file processor.
Running: /amber18/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f acWarning: For atom (ID: 12, Name: OH1) the best APS is not zero. Bonds involving this atom are frozen.
Running: /amber18/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p amberInfo: Total number of electrons: 91; net charge: 0Info: The number of electrons is odd (91). Please check the total charge (-nc flag) and spin multiplicity (-m flag).
Running: /amber18/bin/sqm -O -i sqm.in -o sqm.out/amber18/bin/to_be_dispatched/antechamber: Fatal Error!Cannot properly run "/amber18/bin/sqm -O -i sqm.in -o sqm.out".
I have attached PDB file of residue.Please guide me how to proceed with.
Thanks,Sarah
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- application/octet-stream attachment: HAR.cif
- application/octet-stream attachment: HAR.pdb
Received on Thu Aug 27 2020 - 13:00:02 PDT
