Hi,
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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>>
>
>
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Received on Wed May 16 2012 - 01:00:04 PDT
