Dear Amber !
As suggested in the previous e-mail , I have carried out the gaussian-03
calculation with the input that is being generated by the amber tools
like as below
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
The out put of the gaussian was taken to the antechamber and I followed
the tutorial (
http://sf.anu.edu.au/collaborations/amber_on_fujitsu/amber-12/tutorial/nonstandard-setup/index.html
)
I was able to proceed with all the commands, but the topology file is not
generated
I have the following error
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for OS-CA-CA-CA
atoms are: O7 C11 C10 C9
** Warning: No sp2 improper torsion term for CA-OS-CA-CA
atoms are: C11 O11 C12 C7
** Warning: No sp2 improper torsion term for CA-C-CA-CA
atoms are: C8 C6 C7 C12
** Warning: No sp2 improper torsion term for C-OS-CA-CA
atoms are: C6 O1 C5 C4
** Warning: No sp2 improper torsion term for CA-CA-CA-OS
atoms are: C5 C3 C4 O11
** Warning: No sp2 improper torsion term for CA-CA-CA-CA
atoms are: C4 C13 C3 C2
** Warning: No sp2 improper torsion term for CA-OS-CA-CA
atoms are: C1 O16 C15 C14
** Warning: No sp2 improper torsion term for CA-OS-CA-CA
atoms are: C15 O12 C14 C13
old PREP-specified impropers:
<ROM 1>: C9 C11 C10 O7
<ROM 1>: C12 C10 C11 H5
<ROM 1>: C7 C11 C12 O11
<ROM 1>: C8 C10 C9 H4
<ROM 1>: C9 C7 C8 O6
<ROM 1>: C6 C12 C7 C8
<ROM 1>: C7 C5 C6 O5
<ROM 1>: C6 C4 C5 O1
<ROM 1>: C5 C3 C4 O11
<ROM 1>: C4 C13 C3 C2
<ROM 1>: C3 C14 C13 H6
<ROM 1>: C3 C1 C2 H2
<ROM 1>: C2 C15 C1 H1
<ROM 1>: C1 C14 C15 O16
<ROM 1>: C13 C15 C14 O12
total 7 improper torsions applied
15 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
The molecule of my interest is having the sulfate atoms , when i looked in
to the frcmod file i also found some lines like
O -SO 0.00 0.000 ATTN, need revision
SO-OS 0.00 0.000 ATTN, need revision
I can understand that the bond order, bond angle and the torsion angles
for the S connected to 3 oxygens are not able to be identified by leap ,
how one can proceed with this to fix up the errors
thank you
On Thu, Apr 3, 2014 at 12:26 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Apr 03, 2014, Lara rajam wrote:
> >
> > I am trying to derive the parameter for a molecule ,
> > for that I have carried out the charge calculation using the gaussian03
> > I used the gaussian options as follows
> > #t B3LYP/6-31G* opt freq=noraman
>
> This won't work: you need to request commands to get electrostatic
> potentials.
> You can either:
>
> (1) Study the example in $AMBERHOME/AmberTools/test/antechamber/g09
>
> (which might have to be modified slightly, via the -gv flag, for earlier
> versions of Gaussian);
>
> (2) go to the R.E.D.DB. web site, where there are lots of tools to compute
> resp charges; your molecule may already be in their database.
>
> > is it not possible to generate the library for B3LYP option of the
> gaussian
> > one has to use only HF
>
> It is "possible" to use B3LYP, but the results won't be consistent with
> any of
> the other charges in the Amber force field.
>
> ...dac
>
>
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>
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Received on Mon Apr 07 2014 - 10:30:02 PDT
