On 9/10/13 3:54 PM, Rafael I. Silverman y de la Vega wrote:
How so? If there is an atom type that has a reasonable similarity to the
one that doesnt have the default bondtypes, what makes using that worse
than coming up with entirely new parameters that are not necessarily based
on physical data or quantum calculations? Isnt copying angles and force
constants the same thing?
I never suggested that one should make up parameters that aren't based on
anything. The nonbonded parameters of any force field are highly tuned for
internal consistency, so I was alarmed at the suggestion of simply replacing
atom types. Doing so can very easily perturb the model physics in unpredictable
ways.
Perhaps I should have stated more clearly from the beginning - I never meant to
imply that anyone should simply "add parameters" for a missing interaction.
They must be properly derived. I do maintain (having seen the negative
consequences myself from others' struggles and failed attempts) that replacing
atom types for mere convenience leads to very bad outcomes, probably just as bad
as poorly concocted bonded parameters, if not worse.
It should also be noted that the nonbonded parameters affect torsions, so all of
these terms are, in reality, interrelated. I suspect that the underlying issue
here has been a poorly constructed force field, not parameters that are actually
missing from the model.
-Justin
On Tue, Sep 10, 2013 at 10:34 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote:
Adding parameters can be a little bit of a pain, you could instead change
the atom types in the molecule parameter, to ones that have defined angles
and bond types with each other. Of course, you would need to make sure
that
you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc.
Check out ffbonded in the appropriate forcefield folder to see which
atomtypes have defined bond types. Check out atomtypes.atp to see all the
atom types for the forcefield
Given that at present the issue involves only protein and lipids, the
approach of swapping around atom types is very dangerous, probably more so
than assigning bonded parameters by analogy. I don't recall the OP ever
telling us what the force field is, though, so it's hard to know all of
what we're dealing with here.
-Justin
On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
It is which part in the force field. Exactly which file I have to look
to
overcome this errors.
Go to the line number in the .top indicated in the error message and
determine the atom types. This will tell you the sequence of atom types
involved in the R-B dihedral that is missing. In theory, you would then
add missing parameters to ffbonded.itp, if they exist.
-Justin
On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
This is another type of error while running energy minimization:
what to do for these type of errors.
They're exactly the same as the dihedral error from before. You're
using
parameters that don't exist in the force field.
-Justin
ERROR 218 [file topol.top, line 23487]:
No default Ryckaert-Bell. types
ERROR 219 [file topol.top, line 23499]:
No default Ryckaert-Bell. types
ERROR 220 [file topol.top, line 23500]:
No default Ryckaert-Bell. types
ERROR 221 [file topol.top, line 23501]:
No default Ryckaert-Bell. types
ERROR 222 [file topol.top, line 23502]:
No default Ryckaert-Bell. types
ERROR 223 [file topol.top, line 23503]:
No default Ryckaert-Bell. types
ERROR 224 [file topol.top, line 23515]:
No default Ryckaert-Bell. types
--Rama
On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
I included 1 DMPC molecule parameters in the file should I need to
include
128 molecules parameters in the file .rtp.
No. Residue definitions are used any time they are encountered
in
the
coordinate file. There is no need for such redundancy at the force
field
level.
-Justin
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