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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Received on Sat Jun 22 2019 - 17:30:02 PDT
