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 Wed May 16 2012 - 01:30:02 PDT
