AMBER Archive (2007)

Subject: Re: AMBER:

From: Thomas Pochapsky (pochapsk_at_brandeis.edu)
Date: Fri Aug 10 2007 - 15:34:32 CDT

Steve, I have seen the same thing (with a heme protein, I might
add), but I haven't seen any problem with either watching dynamics
tracks or my usual PDB viewing programs, so I have ignored it. My
heme still looks intact in moilview and in rasmol.
Tom Pochapsky

On Aug 10, 2007, at 4:17 PM, Steve Seibold wrote:

> Hello Amber
>
> I tried to send the attachments, but after one hour they have not
> showed up on the AMBER site and so, I am now sending the following
> message without the attachments.
>
>
>
> I have an unusual problem with xleap or when I make a pdb file
> using “ambdpb”. When I load my initial pdb file (p010A.pdb) into
> xleap and save my topology and coordinate files WITHOUT water my
> output pdb files are fine. However, if I add waters and follow the
> same procedure (i.e. load p010A.pdb and make promtop and inpcrd
> files), I get very strange placements of the “TER” command when I
> construct a pdb file using “savepdb file file.pdb” or “ambpdb”
> commands. Basically it slices up my protein and the heme.
>
>
>
> When I use “desc mol” while using xleap the c-terminal and n-
> terminal are fine with or without water. It is only when I write
> out a pdb file that I get this problem.
>
>
>
> Can someone tell what is going on? Has this happened to someone else?
>
>
>
> Thanks, Steve
>
> P.S.
>
>
>
>
>
>
>
>
>
>

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