AMBER Archive (2002)

Subject: Re: add DUMMY atom into coordinate file

From: Alan Leo (ralyboy_at_sohu.com)
Date: Fri Aug 16 2002 - 14:51:35 CDT

The method of DUMM adding is listed in AMBER5 manual p76, chapter 11, prep.

I am surprised with this why amber7 manual get rid of this part of tree
method.

Good luck!

----- Original Message -----
From: "yuann" <yuann_at_bioinfo.ndhu.edu.tw>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Friday, August 16, 2002 5:12 AM
Subject: add DUMMY atom into coordinate file

> Greetings all,
> I want to create a prep file for an organic molecule about 164 atoms.
> The coordinate was taken from PDB and I used sybyl 6.8 to measure the
> distance, angle, torsion of this molecule. However, I've no idea how
> to add DUMMY atom into coordinate file(i.e. DUMMY atom coordinate in PDB).
> (The 1st atom of this molecule is carbon)
> Except for using Antechamber, is there efficient way to deal with this
> problem or to create prep file ?
> Thanks for your help.
>
> Best Regards,
> sychen
>
>
>