Dear Prof.
Thanks for your answer. I will try with the mol2 file as you said.
David A Case <david.case.rutgers.edu>, 1 Nis 2022 Cum, 15:18 tarihinde şunu
yazdı:
> On Fri, Apr 01, 2022, Erdem Yeler wrote:
>
> >I parameterized Pd atoms with almost all known bonds. For this, I wrote a
> >script to combine gaff and a novel metal force-field (the script can be
> >adapted with Pt, Au, Se, exc...) Everything works perfectly, but there is
> a
> >mini problem: Sander minimized the structure with very high accuracy,
> but Pd
> >lost its bonds and seemed like a "P" atom when I visualized it (I changed
> >the "Pd" sign to "Pm" (because in gaff there is pd even if it it is not
> >exactly Pd with capital P) but I couldn't solve the problem.) Why is this
> >happening? Actually, I don't see it as a serious problem because the
> >minimized geometry is correct, but if there is a way to get rid of this, I
> >am ready to apply.
> >Here is the picture of my molecule: P must be Pd and must have bonds with
> >Cl and N atoms. I checked the prmtop file with parmed. PArmed seed Pd atom
> >and related bonds but after ambpdb commands it seems bond-less P atom...
>
> This looks like a visualization issue; ambpdb does not output CONECT
> records
> unless you use the '-conect' flag. So, the whatever program you are using
> has to guess about what bonds to draw based on interatomic distances.
>
> If parmed says the bonds are there, then the bonds are there. And you
> would
> not get a good geometry if they were absent. Try adding the -conect flag,
> or save your output to mol2 format (which as bond information), assuming
> that your visualization program supports the mol2 format.
>
> ....dac
>
>
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Received on Fri Apr 01 2022 - 06:30:02 PDT
