AMBER Archive (2009)

Subject: [AMBER] pdb file no bond and charges

From: Jio M (
Date: Wed Jul 29 2009 - 01:28:48 CDT

Dear AMBER users,

I made a molecule using different residues. then I dissolved it in water.


After minimization in sander of two steps(solute fixed first then whole
system minimization) I made pdb file by "ambpdb" using rst and prmtop

1) in xleap visualiser there are no bonds seen between atoms. But in
VMD all bonds can be seen. as was mentioned in archive that
bondbydistance command can be used. I used it also in xleap for pdb,
bonds were then visible between atoms but all water molecules became
linear with loss of one hydrogen in all water molecules that is O---H
is shown as a linear. is any thing wrong with visualiser or my
structure. but every thing seems fine in VMD.

2) I also tried to visualise many pdb provided (in tutorial) in xleap
same problem is there i.e. no bonds only dots. bondbydistance shows
bond between atoms but even then some atoms are lying in space
individually with no bond.

3) it is not perfect to use bondbydistance because closer atom will
form a bond even if they are part of different molecules specially in
water molecules as a explicit solvent

4) the minimised structure pdb from sander as I aleady mentioned not
showing bonds but  charges are also not there. every atom charge
is zero. in the pdb if seen as text no charge is there.

from which file the sander will read the charges in next MD run

thanks and pls help me to understand


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