On Mon, Jul 10, 2017, Lizelle Lubbe wrote:
> when visualizing the pdb (saved
> from the prmtop and rst7 of tleap) it doesn't correspond (HD1 sp3, HD2
> sp2, OE1 sp3, ZN sp2, Water sp3).
I'm somewhat confused here: PDB files don't contain any hybridization
information in them. It sounds like you may be describing the
hybridization assigned by the visualization program.
Second, hybridization doesn't matter for force fields once the parameters are
assigned. That is, there is no hybridazation information in a prmtop file
either. You should see if the geometry is reasonable, especially after a
short minimization.
> The atomic_ions.lib file lists Cl- so I assumed this was correct but
> when visualizing the tleap output as pdb (generated from prmtop and
> rst7) in UCSF Chimera and Discovery Studio, the atomtype is given as a
> carbon (sp3) with no formal charge.o
The PDB standard is to put the element into columns 77-78 of the ATOM or
HETATM line. Are you perhaps using an old version of AmberTools? Current
versions (e.g. of ambpdb) should be putting the element information in the
correct line. Use a text editor to check your pdb file, and see if the
element information is in the correct place.
> What is the correct way to insert a chloride ion in AMBER format?
The input pdb file needs to have atom and residue names that match the
atomic_ions.lib file. It sounds like this was the case --otherwise, tleap
would have failed to create the prmtop file. See above for questions about
why your output PDB file may be missing some information. parmed offers a
nice interface to query prmtop files and print out information in them in a
nice format.
...good luck....dac
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Received on Mon Jul 10 2017 - 19:30:02 PDT
