Re: Fwd: vmd-l: Re: hBond colvars and patching

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Fri Mar 11 2011 - 11:40:06 CST

Hi Francesco, if you want to retain the most control on the system, I
suggest that "distance" is the better option. The value of "hBond" would
fall to zero pretty quickly when the distance between the CLA atom and its
ligands increase: but with it being a charged species, the interaction does
instead for longer, and you may want to use a larger distance cutoff (say,
5-6 ) to allow for some rearrangement.

Giacomo

---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
  giacomo.fiorin_at_temple.edu
---- ----

On Fri, Mar 11, 2011 at 10:07 AM, Francesco Pietra <chiendarret_at_gmail.com>wrote:

> Hello Peter:
> Done as you suggested. Now the stereochemistry in the couples
> ASP-patchedGLU, GLU-patchedASP, and CLA-patchedGLU is substantially
> the same before and after unrestricted minimization in a POPC membrane
> (0 K, ts=1, "rigidBonds water", gradient 5.0) and seem palatable. See
> attached examples. I hope the house is in order now.
>
> I found no suggestion from the archives to decide which is best
> appropriate, "distance" or "hBond" colvars, to restrict distances from
> CLA to its ligand atoms (from patchedGLU, LYS, and ARG). Could that be
> suggested? In fact, if the are problems about that, they will only
> emerge from long simulations. My aim is to prevent CLA escaping, while
> allowing formation of the H-bond during equilibration. To this
> concern, it seems to me better not to restrain the GLU-ASP distance or
> hBond, and see what the ff feels. If it is suitable to the system, it
> is a way to see if the H-bond distances seen in the crystal hold for
> the solution state as well in this forced "constant low pH"
> simulation.
>
> Thousand thanks
> francesco
>
>
> On Fri, Mar 11, 2011 at 5:22 AM, Peter Freddolino
> <pfreddol_at_princeton.edu> wrote:
> > Hi Francesco,
> > Could you try building your structure with "Regenerate angles/dihedrals"
> > (under the autopsf Options menu) selected? That should get rid of the
> > odd location of those hydrogens; in some cases psfgen fails to properly
> > add all angle terms that should be present during patching, which would
> > lead to what you saw. Also, the TIP3 topology listed below appears
> > incorrect, as it gets rid of *all* of the bonds. You only need to get
> > rid of the H1-H2 bond, which means deleting the last two words of the
> > BOND line (H1 H2) but uncommenting it.
> >
> > Best,
> > Peter
> >
> > On 03/10/2011 10:45 AM, Francesco Pietra wrote:
> >> Hi Peter:
> >>
> >> With VMD 1.9beta1/Linux
> >>
> >> (1) Open the pdb for protein inserted into POPC (1.5A empty space
> >> between protein and POPC. The latter, preequilibrated was taken from
> >> charmm archives. The protein had been equilibrated at 310K/1atm in
> >> previous work with AMBER10, force field ff99SB.
> >>
> >> (2) Autopsf with top_all27_prot_lipid.rtf, edited as follows
> >> RESI TIP3 0.000
> >> GROUP
> >> ATOM OH2 OT -0.834
> >> ATOM H1 HT 0.417
> >> ATOM H2 HT 0.417
> >> !BOND OH2 H1 OH2 H2 H1 H2
> >>
> >> (2a) Load input files
> >>
> >> (2b) Guess and split chains ....
> >>
> >> segments were correctly identified (P1 for chain A; O1 for CLA in
> >> chain A; P2 for chain B; O2 for CLA in chain B; P3 for chain C; O3
> >> for CLA in chain C; follow O4, O5, etc for POPC and W1..)
> >>
> >> (2c) Create chains
> >>
> >> whereby DISU patches were automatically and correctly applied (the
> >> S...S distances were typical)
> >>
> >> (2d) Apply GLUP and ASPP patches
> >>
> >> which went on correctly as far as OE2 protonation is concerned (some
> >> protons directed toward the acceptor O, some other ones turned back by
> >> 180 deg, as I described previously).
> >>
> >> (2e) Apply patches and finish
> >>
> >> getting psf/pdb.
> >>
> >>
> >> (3) Add solvation box with above psf/pdb; Rotate 10deg; Boundary 2.4;
> >> Use molecule dimensions; Box padding xyz 15 for min and max, followed
> >> by AddIons, salt NaCl, isotonic (0.15M), minimum dist from solute and
> >> between ions 5A, getting final psf/pdb.
> >>
> >> (4) Measuring center and min-max, with the algebraic sum of min-max
> >> for x giving the x cell dimension, and so on for y,z.
> >>
> >> (5) Graphically checking that the patch-added protons were still where
> desired.
> >>
> >> (6) Minimization ts=1fs, no restraints on H, first with protein and
> >> its three CLA restrained, then unrestrained, final gradient 3.0.
> >>
> >> During minimization, the GLU CG-OE2 rotated so that HE2 resulted
> >> closer to the acceptor ASP (actually I have only checked that for one
> >> patched-GLU--ASP in all three subunits).
> >> *****
> >>
> >> This from my notes and fresh memory. Should any doubt arise, or any
> >> modification suggested as to the procedure, or simply a recheck being
> >> desirable, I am here to re-do everything from scratch.
> >>
> >> Thank
> >>
> >> francesco
> >>
> >>
> >> On Thu, Mar 10, 2011 at 3:36 PM, Peter Freddolino
> >> <pfreddol_at_princeton.edu> wrote:
> >>> Hi Francesco,
> >>> I think there may be something seriously wrong with this structure...
> >>> how exactly did you generate it (specifically, the psf)? What topology
> >>> file did you use, and what commands were involved? I do not think the
> >>> proton should be able to reach that position if the topology is correct

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