Re: [AMBER] questions about paramfit and frcmod file

From: ttz <>
Date: Mon, 23 Mar 2020 23:00:34 -0500

   Hi David,

   I got it, thank you so much for looking at the question and your great

   Best regards,


   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:


     -parm <your Amber home directory>/dat/leap/parm/gaff.dat

     -d carbofluid.dat

     -o fit.out



     System Glycerol/coords.cdf Glycerol/energies.dat

     System 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,


   In the above, which is taken from the mdgx tutorial here,, 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 ( 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.



   On Sun, Mar 22, 2020 at 6:11 PM ttz <> wrote:


> Dear all,



> I am currently trying to develop GAFF for cefotaxime using

> 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

> Could anyone help with this? I have attached the original and

> frcmod file, as well as the mol2 file.



> Thanks in advance!



> Best regards,


> Tingting




> Sent from [1]Mail for Windows 10


> References


> 1.

> _______________________________________________

> AMBER mailing list





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Received on Mon Mar 23 2020 - 21:30:02 PDT
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