AMBER Archive (2009)

Subject: Re: [AMBER] creating new residue adds none wanted ter

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Mon May 04 2009 - 09:09:08 CDT

Hi,

I execute

xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03

and then I

loadoff mem.lib

TM = loadpdb nw_prot.pdb

where I have changed the MET to MEM if I then
savepdb TM rs_prot.pdb

I can see in the pdb that it has added the TER to the new residue even
though it is within a given sequence. I don't know if this is all the info I
am rather new to amber so ....

Thanks in advance

Best

On Mon, May 4, 2009 at 3:35 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Mon, May 04, 2009, Jorgen Simonsen wrote:
> >
> > I am trying to create a new residues following the tutorial "*Simulating
> a
> > Solvated Protein that Contains Non-Standard Residues" *where I also have
> MET
> > residue that I have changed to MEM adding an ion to the residue. The
> problem
> > is that when I use ambertool it add a TER to my residue although it is
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
> We need to know details of what commands you gave, what kind of PDB file
> you loaded (if any) and so on. Try to see what you are doing that is
> different from what is Tutorial A1 (Old), since I believe that adds an
> MEM-like residue without the problem you mention.
>
> ..good luck...dac
>
>
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