RE: AMBER: Atoms closer to 2 angstroms to each other

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 7 May 2007 08:30:29 -0700

Dear Christopher,
 
Amber, by which I guess you mean xleap, does not do any connectivity based
on distance. All connectivity for loaded pdb files is based on the templates
that xleap has (from prep and lib files). What is strange is that by adding
the TER card leap shouldn't have bonded across the residues but instead
should have complained about missing atoms that would be capping the groups
in place of the intervening bonds. E.g. If I have a pdb for NGLY-GLY-CGLY
with TER cards between the residues:
 
ATOM 1 N GLY 1 3.326 1.548 0.000
ATOM 2 H1 GLY 1 4.046 0.840 0.000
ATOM 3 H2 GLY 1 2.823 1.500 -0.875
ATOM 4 H3 GLY 1 2.823 1.500 0.875
ATOM 5 CA GLY 1 3.970 2.846 0.000
ATOM 6 HA2 GLY 1 3.672 3.400 -0.890
ATOM 7 HA3 GLY 1 3.672 3.400 0.890
ATOM 8 C GLY 1 5.484 2.687 0.000
ATOM 9 O GLY 1 5.993 1.568 0.000
TER
ATOM 10 N GLY 2 6.203 3.811 0.000
ATOM 11 H GLY 2 5.738 4.708 0.000
ATOM 12 CA GLY 2 7.652 3.794 0.000
ATOM 13 HA2 GLY 2 8.009 3.276 0.890
ATOM 14 HA3 GLY 2 8.009 3.276 -0.890
ATOM 15 C GLY 2 8.200 5.214 0.000
ATOM 16 O GLY 2 7.436 6.177 0.000
TER
ATOM 17 N GLY 3 9.529 5.342 0.000
ATOM 18 H GLY 3 10.115 4.519 0.000
ATOM 19 CA GLY 3 10.173 6.639 0.000
ATOM 20 HA2 GLY 3 9.875 7.194 -0.890
ATOM 21 HA3 GLY 3 9.875 7.194 0.890
ATOM 22 C GLY 3 11.687 6.480 0.000
ATOM 23 O GLY 3 12.196 5.362 0.000
ATOM 24 OXT GLY 3 12.418 7.468 0.000
TER
 
Then xleap believes they are all C terminal Glycines and we get:
 
Created a new atom named: H1 within residue: .R<CGLY 1>
Created a new atom named: H2 within residue: .R<CGLY 1>
Created a new atom named: H3 within residue: .R<CGLY 1>
  Added missing heavy atom: .R<CGLY 1>.A<OXT 8>
  Added missing heavy atom: .R<CGLY 2>.A<OXT 8>
  total atoms in file: 24
  Leap added 3 missing atoms according to residue templates:
       2 Heavy
       1 H / lone pairs
  The file contained 3 atoms not in residue templates
  Since added/missing = extra, there is a high probability
  of atoms with 'incorrect' names; you may want to
  use addPdbAtomMap to map these names, or change in file
 
Then when you look at the structure you see there are all sorts of problems.
 
So to get around this what you need to do is build correct termini for the
ends of your chains and rename the residues appropriately. I assume the
termini will be protonated? Or do you really just want to ignore the bond
that would typically be there but not cap the ends? In this case you can
simply delete this bond in xleap's editor. It would seem to me though that
to get the dynamics correct you will need to explicitly cap the ends of
chains.
 
All the best
Ross

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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Christopher Gaughan
Sent: Monday, May 07, 2007 07:38
To: amber
Subject: AMBER: Atoms closer to 2 angstroms to each other


Dear all,

I am modeling two 28aa artificial peptides that aggregate into a
coiled-coil. To do this I have taken the side chains off tropomyosin and
replaced them with the side chains of interest. In one model I have the two
strands of tropomyosin composed of 8mers- specifically- strand one is
composed of an 8mer of the type 1 peptide and strand 2 is composed of an
8mer of the type 2 peptide. I would like to put a TER card after each 28aa
mer in each strand to simulate the strand being composed of 8 distinct
units. When I do so, Amber just reconnects them. I assume this is because
the consecutive C and N termini I wish to simulate are too close together.
Is there any way I can get around this automatic feature (connecting atoms
that are very close) in AMBER 8?

Thanks for any advice,
Chris






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