On Tue, Oct 13, 2015 at 2:08 PM, Hadeer ELHabashy <
hadeer.elhabashi.gmail.com> wrote:
> Dear Sir
>
> wish you are fine !
>
> I have a pdb file consists of four identical peptides and I want to
> simulate them together. However Amber can not detect many atoms with
> similar names or similar residue number.
This is not quite true. What *is* true is that tleap cannot determine
that you intended to start a new residue when the residue name *and* number
is identical to the previous residue. It is also true that tleap matches
residue templates to residues in input structures in order to assign
parameters, and as a result of this each atom's name must be unique in the
residue. As long as two atoms do not have *exactly* the same names, then
tleap will distinguish between them. If two atoms *do* have exactly the
same name, then only the first atom with that name will be taken.
Note that this behavior is very common in MD packages (which often have to
read PDB files that contain duplicate atoms specifying alternate
conformers, from which only one conformer should be simulated). If your
input files define residues that have duplicate atom names (*exact*
duplicates, not just "similar"), then you have to change this before Amber
will treat it the way you want it treated.
This means that you need to make sure that atom names are unique in a
residue in *both* the PDB file and the residue template library (i.e., mol2
or OFF library file), and moreover that those atom names match each other.
Your description ("Amber can not detect many atoms with similar names or
similar residue number") is overly general and vague, which makes it
impossible for me to identify your actual problem with any certainty.
> I have tried to change the atoms
> names or the residues names but xleap has many problem with this and some
> structure deformation happened .
Again, this lacks details. "structure deformation" can mean many things.
Here are some examples that I've seen: a file mismatch in visualization (
http://archive.ambermd.org/200707/att-0208/b1_md2_181.jpg
), a possibly surprising representation of a "boiling" system under very
low pressures (
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-9267/Opt-solv.png),
functional groups collapsed to a single point when taking an average
structure, PBC imaging artifacts (
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-9267/Min-2.png),
a methyl group forced through the center of a benzene ring in a
poorly-parametrized ligand with a bad starting geometry, ...
Every one of those examples has a drastically different underlying cause
and has a different solution. Without knowing what exactly you did, it's
impossible to guess where the problem is. It could be in your residue
template file, your PDB file, or both, potentially. So we really need more
details (very specific details) in order to help here.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 13 2015 - 12:00:03 PDT
