From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Oct 17 2014 - 03:12:48 CDT
> believe you might have misinterpreted the CGenFF output. By default, it
> outputs only the parameters that are not already in the main parameter file
I have misinterpreted it indeed. Thanks for pointing out this major mistake
from my side, related to the only statement in the .str file about bonds:
CG2RC0 NG2R61 370.00 1.3790 ! /scrat , from CG2R61 NG2RC0, penalty= 30
This is formally a C-N single bond, like in histidine (the molecule could
be seen as a fused combination of uracil and monoprotonated histidine)
Now, I have to study the published notes about CGenFF as to how its output
can be improved. Through ffTK only? Incidentally, how to get the a correct
residue name instead of
RESI /scratch 0.000 !
By just manually replacing /scrat?
this is fundamentally wrong. Bonded parameters (especially the dihedrals)
> only work in combination with the 1-4 and longer-range electrostatic
> interactions against which they were parameterized.
It was implied (or stated?) in my reasoning that I reshape the antechamber
output to deal with the 1-4 affair. If I was not wrong in doing that.
Relative to ffTK, how time-consuming would you say preparing, setting up,
> running and analyzing an MD simulation is?
You are quite wright, and I am prepared to spend time, all required time,
to stay along a sound way. Thus, it is not the time, per se, that ffTK
requires. It is that I found it difficult to get the procedure running,
saving, resuming. I had often to start again from scratch. I completed some
cases of my interest, but something came out in error, such as certain
impossible values of charges or dihedrals. A bit more automation,
especially with drihedrals would help.
Straightforward with normal proteins, the problems come
> with organic ligands, not to say with metalloproteins.
To such a vague accusation, we can only reply equally vaguely that our
> software is more honest than most
Let me say that I prefer psfgen by far, and not only as it leaves the
residue numbers unchanged. When dealing with pure proteins, or
metalloproteins with ts metal centers already parameterized, such as with
heme proteins, no problem. The problems I alluded to come with, say, non
heme iron proteins, where even problems of antiferromagnetic coupling
between irons might be involved. Here antechamber has no room, still amber
has some working tools. In that case, obviously I have to stay wholly with
amber ff, although running it through namd (hopefully this is a sound way,
someone along the amber forum some time ago raised doubts about running
amber ff with namd).
In conclusion, I have planned to learn better about CGenFF, ffTK and the
various psfgen tutorials about metalloproteins. Just working about the
uracil-histidine I alluded to above. The biochemist with mostly an
experimental background tends to spend time about the chemical problem,
overlooking the protocol for the simulations.
On Fri, Oct 17, 2014 at 12:53 AM, Kenno Vanommeslaeghe <
> On 10/16/2014 05:41 PM, Francesco Pietra wrote:
>> Again to CGenFF after a long while, I was terrorized by the complexity of
>> symbols for atom types of organic molecules (protein ligands).
> True, it's pretty complex indeed. That's exactly why we have encoded the
> atom typing rules in the CGenFF program at paramchem.org . It gets it
> right more often than I manage to do manually.
> Also, for
>> ligands not too far away from purine bases, CGenFF performed quite
>> naively, for example, giving a single Kb for bonds
> I believe you might have misinterpreted the CGenFF output. By default, it
> outputs only the parameters that are not already in the main parameter
> file, so if it outputs a single parameter, that simply means all the other
> parameters are in the main file. And I'm quite certain it doesn't use the
> same bond parameter for C=O and C-C bonds; if it does, you should report
> that as a bug. Conversely, if the problem is simply that the parameters go
> against your intuition, then you probably should show they're misbehaving
> in an actual simulation scenario.
> So, I built bonds, angles, dih,
>> impr from antechamber. Then, apart from the problem of charmm-type partial
> As I've repeated countless times on this list, this is fundamentally
> wrong. Bonded parameters (especially the dihedrals) only work in
> combination with the 1-4 and longer-range electrostatic interactions
> against which they were parameterized. If you're going to use antechamber
> for your bonded parameters, then you HAVE to use GAFF atom types and
> charges, and an Amber representation for the rest of your system
> I tried a couple of times ffTK
>> just to be on an absolute basis, a very nice suite but extremely time
>> consuming. Nothing good comes for little, however.
> True. Relative to ffTK, how time-consuming would you say preparing,
> setting up, running and analyzing an MD simulation is?
> Straightforward with normal proteins, the problems come
>> with organic ligands, not to say with metalloproteins.
> To such a vague accusation, we can only reply equally vaguely that our
> software is more honest than most about the quality of the parameters it
> produces, and that it will flat-out refuse to generate a model that would
> likely be deeply flawed, reflecting our philosophy in releasing force
> If you're talking specifically about heme, you'll find the same heme model
> you mentioned before in the CHARMM36 tarball.
> In that respect,
>> which is nearly the norm for me, amber offers easier tools
> No problem, we'll be just as happy if you choose to use amber. As long as
> you don't mix them. ;)
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