AMBER Archive (2009)

Subject: Re: [AMBER] (no subject)

From: Jenny Iskrenova (
Date: Fri Jan 16 2009 - 12:42:08 CST


I have the same problem. Although I start with a good structure. The
structure was created and the geometry was optimized in Materials
Studio. I load the good initial pdb file in LeAP and add ions. Then I
create the inpcrd and prmtop files. When viewed with VMD, the
structure in the inpcrd file is distorted -- some of the bonds are
really stretched.

After solvating, I perform equilibration runs. Then, I proceed with
minimization runs. At the end of all this initial equilibration and
minimization, the structure looks reasonable. I haven't done the
"bring the atoms slowly together" trick with nmropt=1. There are not
just two atoms that are too far apart. My molecule is an acetate ion.
I suppose, for such a small molecule, one can afford longer
equilibration/minimization runs. But is this enough?


On Fri, Jan 16, 2009 at 12:43 PM, Carlos Simmerling
<> wrote:
> leap can add the bond, but that doesn't automatically change the
> peptide conformation to make the bond short. all leap will do is take
> the conformation that you loaded or built, and create a bond. you will
> need to minimize this or do some work in building your initial
> conformation to get it right.
> note that minimizing a long bond is VERY likely to cause other
> problems, since the energy will eb high enough to invert chiralities,
> flip amides and so on.
> I suggest that if you don't have a good conformation to start with,
> that you build it without the cyclic bond, and then create a distance
> restraint in sander for these 2 atoms. then, use nmropt=1 to slowly
> draw them together during MD, with a final distance the same or close
> to the bond length. take the final structure, convert to pdb, and use
> that as the initial structure for the prmtop that has the bond
> defined.
> On Fri, Jan 16, 2009 at 12:38 PM, Lake, Thomas
> <> wrote:
>> Hello,
>> I am trying to model a cyclic peptide, so I loaded the pdb into LEAP. I
>> then created a bond between the two terminal residues, and then altered
>> the partial charges and the atom types of these residues. In LEAP this
>> seemed to work fine; I then created topology and coordinate files using
>> saveamberparm. However when I loaded these into VMD, the bonds where
>> the termini were linked are now massively distorted. In the LEAP editor
>> there doesn't seem to be this problem. Can anyone help me.
>> Thanks
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