Dear Friends,
I like to do ESP on a sodium cluster.I have installed amber 22.0 defaultly.When i try to run a sodium cluster geometry coordinates,I am getting this error.From This i understood that i have to add bond types for sodium by freezing the bond types.Can any one tell how to do this freezing this bond types?
(base) user.lynch:~/siva/gromacs/ test$ antechamber -i Na_20.gcrt -fi gcrt -o Na_20.gout -fo gout
Welcome to antechamber 22.0: molecular input file processor.
Info: acdoctor mode is on: check and diagnose problems in the input file.
Info: The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
-- Check Unusual Elements --
Warning: Unusual element (Na) for atom (ID: 1, Name: Na1).
Warning: Unusual element (Na) for atom (ID: 2, Name: Na2).
Warning: Unusual element (Na) for atom (ID: 3, Name: Na3).
Warning: Unusual element (Na) for atom (ID: 4, Name: Na4).
Warning: Unusual element (Na) for atom (ID: 5, Name: Na5).
Warning: Unusual element (Na) for atom (ID: 6, Name: Na6).
Warning: Unusual element (Na) for atom (ID: 7, Name: Na7).
Warning: Unusual element (Na) for atom (ID: 8, Name: Na8).
Warning: Unusual element (Na) for atom (ID: 9, Name: Na9).
Warning: Unusual element (Na) for atom (ID: 10, Name: Na10).
Warning: Unusual element (Na) for atom (ID: 11, Name: Na11).
Warning: Unusual element (Na) for atom (ID: 12, Name: Na12).
Warning: Unusual element (Na) for atom (ID: 13, Name: Na13).
Warning: Unusual element (Na) for atom (ID: 14, Name: Na14).
Warning: Unusual element (Na) for atom (ID: 15, Name: Na15).
Warning: Unusual element (Na) for atom (ID: 16, Name: Na16).
Warning: Unusual element (Na) for atom (ID: 17, Name: Na17).
Warning: Unusual element (Na) for atom (ID: 18, Name: Na18).
Warning: Unusual element (Na) for atom (ID: 19, Name: Na19).
Warning: Unusual element (Na) for atom (ID: 20, Name: Na20).
/opt/amber22/bin/wrapped_ progs/antechamber: Fatal Error!
GAFF does not have sufficient parameters for molecules having unusual
elements (those other than H,C,N,O,S,P and halogens).
To ensure antechamber works properly, one may need to designate
bond types for bonds involved with unusual elements.
To do so, simply freeze the bond types by appending "F" or "f"
to the corresponding bond types in ac or mol2 files
and rerun antechamber without unusual element checking via:
antechamber -dr no
Alternatively for metals, see metalpdb2mol2.py in MCPB.
Regards,
Sivasanker K A
NCL ID-12183
c/o Dr. Kumar Vanka
Physical & Material Chemistry
CSIR NCL Pune
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Received on Fri Sep 22 2023 - 02:00:02 PDT
