Dear Prof. Francois
I have used the online R.E.D. server and it is giving an error of checking
charge and spin multiplicity. Can you please suggest me something how can I
remove this error.
My p2n file looks like:
REMARK
REMARK TITLE MOLECULE
REMARK CHARGE-VALUE 0
REMARK MULTIPLICITY-VALUE 1
REMARK
ATOM 1 C1 STE 0 19.858 23.775 32.267 C
ATOM 2 C2 STE 0 19.387 25.138 31.862 C
ATOM 3 C3 STE 0 19.921 22.874 31.041 C
ATOM 4 C4 STE 0 21.304 23.857 32.738 C
ATOM 5 C5 STE 0 19.137 25.435 30.583 C
ATOM 6 C6 STE 0 18.666 26.798 30.177 C
ATOM 7 C7 STE 0 19.339 27.848 31.051 C
ATOM 8 C8 STE 0 20.933 21.801 31.423 C
ATOM 9 C9 STE 0 19.197 26.147 32.951 C
ATOM 10 C10 STE 0 19.303 24.418 29.498 C
ATOM 11 C11 STE 0 19.024 27.045 28.719 C
ATOM 12 C12 STE 0 20.448 23.669 29.854 C
ATOM 13 C13 STE 0 18.966 27.614 32.508 C
ATOM 14 C14 STE 0 18.878 29.236 30.624 C
ATOM 15 C15 STE 0 21.946 22.541 32.287 C
ATOM 16 C16 STE 0 21.620 21.280 30.168 C
ATOM 17 C17 STE 0 18.562 28.437 28.311 C
ATOM 18 C18 STE 0 19.251 29.467 29.175 C
ATOM 19 C19 STE 0 22.631 20.207 30.550 C
ATOM 20 C20 STE 0 21.915 19.059 31.251 C
ATOM 21 C21 STE 0 22.858 17.959 31.659 C
ATOM 22 C22 STE 0 22.288 16.762 32.361 C
ATOM 23 C23 STE 0 20.803 16.717 32.599 C
ATOM 24 C24 STE 0 17.367 29.340 30.783 C
ATOM 25 C25 STE 0 18.526 22.351 30.723 C
ATOM 26 C26 STE 0 17.156 26.885 30.352 C
ATOM 27 C27 STE 0 18.888 23.184 33.282 C
ATOM 28 C28 STE 0 22.335 22.426 29.465 C
ATOM 29 C29 STE 0 19.555 30.286 31.496 C
ATOM 30 C30 STE 0 23.241 15.819 33.044 C
ATOM 31 N31 STE 0 22.553 16.767 30.916 N
ATOM 32 H31 STE 0 23.415 16.255 30.726 H
ATOM 33 O32 STE 0 18.756 30.746 28.802 O
ATOM 34 H32 STE 0 19.192 31.379 29.347 H
CONECT 1 2 3 4 27
CONECT 2 1 5 9
CONECT 3 1 8 12 25
CONECT 4 1 15
CONECT 5 2 6 10
CONECT 6 5 7 11 26
CONECT 7 6 13 14
CONECT 8 3 15 16
CONECT 9 2 13
CONECT 10 5 12
CONECT 11 6 17
CONECT 12 3 10
CONECT 13 7 9
CONECT 14 7 18 24 29
CONECT 15 4 8
CONECT 16 8 19 28
CONECT 17 11 18
CONECT 18 14 17 33
CONECT 19 16 20
CONECT 20 19 21
CONECT 21 20 22 31
CONECT 22 21 23 30 31
CONECT 23 22
CONECT 24 14
CONECT 25 3
CONECT 26 6
CONECT 27 1
CONECT 28 16
CONECT 29 14
CONECT 30 22
CONECT 31 21 22 32
CONECT 32 31
CONECT 33 18 34
CONECT 34 33
END
Best Regards,
Asma
On Wed, May 16, 2012 at 1:29 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Asma,
>
> You might try R.E.D. Server, which interfaces the Gaussian, GAMESS or
> Firefly program and the RESP program. See
> http://q4md-forcefieldtools.org/
>
> regards, Francois
>
>
> > I have followed the examples and used the smaller molecule for the
> creation
> > of topology and coordinate files, it works fine but I am required to
> > perform the simulation of our docked complex that we generated through
> > experimental studies. What possibly can be the errors in the structure
> that
> > prevent sqm from running? How can I give the charge of the molecule, or
> > work out the missing hydrogen(s)?
> >
> >
> >
> > On Wed, May 16, 2012 at 11:17 AM, Asma Abro 28-FBAS/MSBI/F09 <
> > asma.msbi28.iiu.edu.pk> wrote:
> >
> >> Yeah I am sorry, my mistake.
> >>
> >> Ok I am following the examples and would write if i get errors again.
> >>
> >> thanks
> >>
> >>
> >> On Wed, May 16, 2012 at 10:52 AM, case <case.biomaps.rutgers.edu>
> wrote:
> >>
> >>> On Wed, May 16, 2012, Asma Abro 28-FBAS/MSBI/F09 wrote:
> >>>
> >>> > The same error message which I was getting using Amber10, i am
> getting
> >>> with
> >>> > Amber12.
> >>>
> >>> Well, in my defense, the error message you post below is completely
> >>> different from the message you posted here:
> >>>
> >>> http://archive.ambermd.org/201205/0327.html
> >>>
> >>> Sorry if I missed something.
> >>>
> >>> > Running: /home/.../AMBER/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0
> -o
> >>> > ANTECHAMBER_AC.AC -p gaff
> >>> > Total number of electrons: 247; net charge: 0
> >>> > INFO: Number of electrons is odd: 247
> >>> > Please check the total charge (-nc flag) and spin multiplicity
> (-m
> >>> > flag)
> >>>
> >>> Things look fine, except that antechamber's bcc procedure is limited to
> >>> closed
> >>> shell molecules. You are giving it a molecule with an odd number of
> >>> electrons. Either you have neglected to give the charge of the
> molecule,
> >>> or
> >>> you are missing hydrogen(s), or something else. Since you are new to
> all
> >>> this, I'd suggest starting with a smaller molecule to gain experience,
> >>> then
> >>> work up to the one you really want.
> >>>
> >>> ....dac
>
>
>
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Received on Thu May 31 2012 - 02:30:03 PDT
