I am not understanding why you need GAFF here, and why you mention bonds.
It seems to me that sodium should not have "bonds" between the atoms. As
Anselm mentioned, simulation of metallic solids is not likely to be very
accurate using simple classical force field. I think you should take a step
back and decide what description of the system is adequate before trying to
run antechamber.
On Fri, Sep 22, 2023 at 7:21 AM K A SIVASANKER via AMBER <amber.ambermd.org>
wrote:
> Dear Dr.Horm,
> Thank you for the suggestion.I do know how to add ions(amber manual
> chapter 3.6).But i want to add GAFF onto Na_20 cluster and do a MD
> simulation of the cluster
> in a water shell using gromacs.I don't know how to freeze the bond
> types.Can you suggest where i can read about it? some reference about
> it..Can you tell how to do freeze the bond types and what edit i have to
> add in the mol2 files?
>
> Regards,
>
> Sivasanker K A
> NCL ID-12183
> c/o Dr. Kumar Vanka
> Physical & Material Chemistry
> CSIR NCL Pune
>
> ----- Original Message -----
> From: amber.ambermd.org
> To: amber.ambermd.org
> Sent: Friday, September 22, 2023 3:17:39 PM
> Subject: Re: [AMBER] How to designate the Bond type(Sodium) in amber 22
>
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Fri Sep 22 2023 - 05:00:02 PDT
