ok thank you
On Sun, Jun 23, 2019 at 1:26 AM <zmatovic.kg.ac.rs> wrote:
> There is no need for sqm.pdb file...it's just a file visible after AM1
> after min process what's up to me... and only relevant file for u is
> BG6_amber.mol2 which is OK....I've checked it up..btw in opt process
> phosphate oxygen somehow O2P has attracted H from OH group but it doesn't
> mean big deal as I said u do not need this file; mol2 file has everything
> you need for.
>
> Cheers
> Zoran
>
> -----Original Message-----
> From: Sadaf Rani <sadafrani6.gmail.com>
> Sent: Saturday, June 22, 2019 5:36 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] sqm.pdb structure
>
> Dear Zoran
> Sorry here is the sqm output file
> here 1 of H from ring Oxygen moved to Phosphate Oxygen.
> please suggest
> thank you
>
> On Sat, Jun 22, 2019 at 4:19 PM <zmatovic.kg.ac.rs> wrote:
>
> > "I am trying to generate parameters for my ligand when I submit the
> > following command antechamber -i BG6_noH.mol2 -fi mol2 -o
> > BG6_amber.mol2 -fo mol2 -c bcc -pf yes -nc -2 -at gaff2 -j 4
> >
> > I get the structure which is different from the submitted one.
> > I wonder which structure I need to use in tleap because the
> > BG6_amber.mol2 is not right I am a little bit confused why it has
> > changed and for which it has generated parameters either for
> BG6_noH.mol2 or BG6_amber.mol2."
> >
> > I do not see different structures instead they are exactly the same
> > with just new charges according to the method chosen. Please be more
> > explicit in defining the problem.
> >
> > Zoran
> >
> >
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>
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Received on Mon Jun 24 2019 - 02:00:02 PDT
