Dear Asma,
- you need to generate the P2N file (R.E.D. input) using Ante_R.E.D. 2.0
- then hydrogens are missing in your structure.
See
http://q4md-forcefieldtools.org/REDS/faq.php#20
regards, 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 - 03:00:03 PDT
