Dear Pengfei and David,
Thanks for the helpful information.
> 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?
I am using AmberTools 15
>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.
Yes, I was describing the visualization program's assignment, but it probably doesn't matter then since I'm using the mol2 and frcmod from MCPB.py
> Use a text editor to check your pdb file, and see if the element information is in the correct place.
I've checked the leap input pdb file again and although it all seems to be fine (changed Cl- to CL in column 77) it still displays a carbon.
HETATM12492 H2O 0fA 720 -35.331 -14.332 -7.397 1.00 0.00 H
TER
HETATM12493 ZN ZN1 721 -27.766 -21.998 -36.628 1.00 0.00 ZN
TER
HETATM12494 CL CL 722 -18.015 -27.711 -36.880 1.00 0.00 CL
TER
ATOM 12495 O WT1 723 -27.107 -20.515 -34.545 1.00 0.00 O
After running pdb4amber on it, however, it correctly displays a chlorine ion
Using this as input for leap gives pdb output files that correctly display a chloride ion with formal charge of -1. The corresponding prmtop and rst7 visualization in VMD still gave C with no charge. Could you please help me to understand why this is the case? Would the ff14SB forcefield correctly type CL instead of C during the MD?
Kind regards
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
________________________________________
From: David Case <david.case.rutgers.edu>
Sent: 11 July 2017 04:05:39 AM
To: AMBER Mailing List
Subject: Re: [AMBER] tleap atom type and hybridization
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 Tue Jul 11 2017 - 04:00:03 PDT
