Hello all.
When i did ligand topology files by using acpype in few cases a got error, below.
/home/work/fast/VV/gromacs/acpype/acpype.py -i Ligand.pdb
===============================================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2014-08-27 18:33:45Z Rev: 403 (c) 2014 AWSdS |
===============================================================================================
==> ... charge set to 0
==> ... converting pdb input file to mol2 input file
==> * Babel OK *
==> Executing Antechamber...
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Running: /usr/local/ambertools/amber12//bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /usr/local/ambertools/amber12//bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 293; net charge: 0
INFO: Number of electrons is odd: 293
Please check the total charge (-nc flag) and spin multiplicity (-m flag)
Running: /usr/local/ambertools/amber12//bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/usr/local/ambertools/amber12//bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
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Cannot open file Ligand_bcc_gaff.mol2 to read in rmol2(), exit
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> ... trying Sleap
==> Executing Sleap...
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++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: 1: -f: not found
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ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'Ligand_AC.prmtop'
Total time of execution: less than a second
dikov@entry1:/home/work/fast/VV/gromacs/md/c-src$
I've already update AmberTool, but it didn't help. Does anybody know how to fix such problem with the ligand ? I would be very grateful for any assistants.
I could be wrong, but it looks like the program is choking on the odd number of electrons. once it fails the parameter check, none of the other types of processing work. it just falls through them with errors. to get it to work, offer it an even number of electrons, is my guess. Alternately change the charge value to indicate that there is an odd number of electrons. I think it is trying to tell you that you can't have an odd number of electrons, and a 0 charge.
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