On 17/08/2012 2:56 PM, shahid nayeem wrote:
I want to simulate without building the missing residue. Does gromacs
have an option of capping. I am using Gromacs 4.5.4. If not then
suggest some software which I may use.
All you can do is use pdb2gmx as you do for the normal termini. pdb2gmx
-chainsep helps you choose where the extra termini go. pdb2gmx -h is
your friend.
Mark
Shahid nayeem
On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote:
On 17/08/2012 2:28 PM, shahid nayeem wrote:
Right, I have a pdb where some of the residues are missing and when I
try to simulate it I get LINCS warning in between the atom of the two
ends of missing residues. So if I use a smaller time step (0.01) for
final production run and energy minimization with setting constraint =
none, making it computationally more expensive. Will these results
will be O.K.
Does it sound OK to model missing residues with solvent (or vacuum) and have
a chemical bond between the dangling ends? It's also definitely not OK to
ignore the warning pdb2gmx gave you about this bond being too long. Plowing
ahead blindly costs more time than than being careful and painstaking.
You need to either cap your chains or build in the missing residues with
non-GROMACS software, but what's best depends what you're trying to observe.
Mark
Shahid Nayeem
On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham <mark.abra...@anu.edu.au>
wrote:
On 17/08/2012 2:02 PM, shahid nayeem wrote:
Dear all
One basic clarification. How does LINCS algorithm influences the
results
of final production run. In what respect a minimization, pr and final
simulation done with constraints = none and with constraint= all_bonds
are
different.
Sounds like you should do some background reading on how and why
constraints
work. Manual and refs therein are good starting points. Or your favourite
molecular simulation textbook. In a nutshell, you use them in production
simulation because they're a reasonable model and allow a larger time
step.
You might avoid them when you're not yet at equilbrium, because their
implementation can be brittle when your structure doesn't agree with the
model physics.
Mark
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