Hi David,
I got it, thank you so much for looking at the question and your great
suggestions!
Best regards,
Tingting
Sent from [1]Mail for Windows 10
From: [2]David Cerutti
Sent: Monday, March 23, 2020 1:37 AM
To: [3]AMBER Mailing List
Subject: Re: [AMBER] questions about paramfit and frcmod file
If you remove certain terms form the frcmod that were necessary to complete
the topology, then tleap will tell you that it couldn't find the
information it needed (you took it away). There is probably a way in
paramfit to mask out certain dihedrals, but I can only tell you about mdgx,
which is the program that Amber will be putting forward for optimizing
dihedral angles starting in Amber20.
The way to do this in mdgx is to make a trajectory, with all the
configurations of your molecule, a prmtop for that trajectory, and a file
listing the QM energies of each configuration, one per line. You need only
make the prmtop once, so long as you are not changing atom types and you
are merely adjusting the stiffness constants of the dihedrals.
Then, you will make a file something like this:
&files
-parm <your Amber home directory>/dat/leap/parm/gaff.dat
-d carbofluid.dat
-o fit.out
&end
¶m
System Glycerol_vac.top Glycerol/coords.cdf Glycerol/energies.dat
System MPD_vac.top MPD/coords.cdf MPD/energies.dat
ParmOutput frcmod
eunits hartree,
accrep report.m
verbose 1,
% Angle fitting input
fita c3 oh ho
fita c3 c3 oh
fita c3 c3 c3
FitAnglEq 1,
arst 0.0002,
arstcpl 1.0,
% Torsion fitting input
fith c3 c3 c3 c3
fith hc c3 c3 oh
fith hc c3 c3 c3
fith oh c3 c3 oh
fith h1 c3 c3 oh
fith X c3 oh X
fith c3 c3 oh ho
hrst 0.0002,
&end
In the above, which is taken from the mdgx tutorial here,
http://ambermd.org/tutorials/advanced/tutorial32/, I have give it two
trajectories for two different systems that contain instances of the same
parameters. I then enumerated the parameters with the "fith" keyword
(alias FitH, meaning Fit DIHEDRAL). There is also fita, which is Fit
ANGLE. The four atom types for the relevant dihedral follow. The hrst
setting of 0.0002 is a good value to start with--this is the normalization
towards zero, a harmonic restraint imposed on each parameter to penalize it
having any value at all. The setting of 0.0002 will have the same effect
on your results no matter how big your data set--it scales with the number
of data points and the number of places each parameter appears in them.
What you'll do is make your trajectories, energy lists, and prmtops, then
run mdgx on input like this to get a new frcmod file (the file name is the
-d keyword up in the &files namelist). Then, it's like sander, mdgx -O -I
fit.in (fit.in is your input file), and read through the fit.out to see
what mdgx thinks of your data set. If you want to optimize thirty
dihedrals that's a lot, but mdgx will let you know if your data set is up
to the job and help you expand it if that's what you really want to do.
HTH,
Dave
On Sun, Mar 22, 2020 at 6:11 PM ttz <tzhao97.gmail.com> wrote:
>
> Dear all,
>
>
> I am currently trying to develop GAFF for cefotaxime using
“paramfits”.
> There are more than 30 dihedral angles need to be optimized, so I
> decided
> optimized the dihedral angle parameters of one subgroup first(10
> dihedral
> angles). After finishing this part, I want to keep those optimized
> parameters and then optimize another subgroup. So I change the
> parameters in
> the frcmod file to generate prmtop file, but there are errors saying
> that
> “ Error: ** No torsion terms for cc-cd-cf-n2, Error: ** No torsion
> terms
> for cc-ss-cc-cd”. However, there parameters do exit in the frcmod
file.
> Could anyone help with this? I have attached the original and
modified
> frcmod file, as well as the mol2 file.
>
>
> Thanks in advance!
>
>
> Best regards,
>
> Tingting
>
>
>
> Sent from [1]Mail for Windows 10
>
> References
>
> 1. https://go.microsoft.com/fwlink/?LinkId=550986
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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References
1.
https://go.microsoft.com/fwlink/?LinkId=550986
2. mailto:dscerutti.gmail.com
3. mailto:amber.ambermd.org
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Received on Mon Mar 23 2020 - 21:30:02 PDT
