Sivasanker,
it is not completely clear to me, what you intend to do, so I can only
guess that you are trying to create (R)ESP atomic charges for a sodium
cluster.
For monovalent ions there are already different parameter sets
available, which can be used in structure optimization and molecular
dynamics simulation with different force fields; have a look in the
Amber manual about that.
To simulate an isolated cluster of metal ions, AMBER force fields may be
not the ideal choice, since the focus is on biomolecules. Quantum
chemistry is better suited to describe such a system.
(Anyway: antechamber seems to output how to freeze the bond types;
convert your input file to ac or mol2 format, edit that file, and rerun
antechamber.)
Good luck,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 22.09.2023 um 10:51 schrieb K A SIVASANKER via AMBER:
> 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 - 03:00:01 PDT
