Date: Fri, 1 Apr 2022 12:18:16 +0300
*sorry not "parmed seed" it is "parmed sees".
Erdem Yeler <erdemyeler.gmail.com>, 1 Nis 2022 Cum, 12:17 tarihinde şunu
yazdı:
> Hello amberers,
> 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...
> [image: image.png]
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/png attachment: image.png)
