Hello everyone,
I'm working in a parametrization of molecules with paramfit, and I discover
now what’s going wrong, but I can’t solve it. Maybe you can see the
problem, cause I ran out of ideas.
I need to vary some angle, for example, so, for this, employ impose
function of tleap. When I tried to parametrize each parameter, I finded
errors in three of them, and basically the impose function doesn’t work in
then. It isn’t problems in my .mol2 or .frcmod files, cause same files
worked fine for imposing in different angles/dihedrals.
I tried to generate those different angles with impose by hand (and
following amber manual of impose function), for maybe detecting errors in
the script, but unsuccessfully.
At amber manual, for impose: “Three types of conformational change are
supported: Bond length changes, bond angle changes, and torsion angle
changes.” So, this part is ok.
And: “If at any point, the impose command does not find an atom bonded to a
previous atom in an internals list, it will silently ignore the command.
This is likely to occur in two instances. One, the atom simply might not
exist, [...] Similarly, improper torsions are ignored.” And in this point,
I double checked the atom names, and the addition of new atom types (cause
they are necessary in my case). And when happend with one dihedral, it
wasn't a improper one.
Someone can find what’s going wrong?
Thanks in advance!
Follow my attempts:
**m1.mol2:.<TRIPOS>MOLECULEM1 14 13 1 0 0SMALLresp@<TRIPOS>ATOM
1 H1 3.2200 -0.7250 0.0000 hc 1 M1 0.060395 2
C1 2.4700 0.0700 0.0000 c3 1 M1 -0.279014 3 C2
1.0580 -0.4940 -0.0000 c3 1 M1 0.303611 4 H2
2.6440 0.6930 -0.8820 hc 1 M1 0.060395 5 H3
2.6440 0.6930 0.8820 hc 1 M1 0.060395 6 CJ3
-0.0180 0.5890 -0.0000 J3 1 M1 -0.339895 7 H4
0.9260 -1.1410 0.8740 hc 1 M1 -0.054885 8 H5
0.9260 -1.1410 -0.8740 hc 1 M1 -0.054885 9 H6
0.1020 1.2390 0.8750 hc 1 M1 0.061974 10 SI
-1.7740 -0.0750 -0.0000 SI 1 M1 0.739284 11 H7
0.1020 1.2390 -0.8750 hc 1 M1 0.061974 12 H8
-2.0140 -0.9160 1.2060 ha 1 M1 -0.206450 13 H9
-2.0140 -0.9180 -1.2050 ha 1 M1 -0.206450 14 H10
-2.7630 1.0370 -0.0000 ha 1 M1 -0.206450@<TRIPOS>BOND
1 1 2 1 2 2 3 1 3 2 4 1 4 2 5 1 5 3
6 1 6 3 7 1 7 3 8 1 8 6 9 1 9 6 10 1
10 6 11 1 11 10 12 1 12 10 13 1 13 10 14 1
.<TRIPOS>SUBSTRUCTURE 1 M1 1 TEMP 0 **** **** 0
ROOT*m1.frcmod:remark goes hereMASSSI 28.08
SiJ3 12.01 0.878 c3 gaff.datBONDc3-J3
305.5 1.6076 paramfit plusdef/fit_4 R^2 0.9264J3-hc 353.9
1.1784 paramfit plusdef/fit_4 R^2 0.9264J3-SI 173.0 1.9811
paramfit plusdef/fit_4 R^2 0.9264SI-ha 239.0 1.4600
SI-ha m1.itp GROMOS54A7, ATBANGLEc3-c3-J3 62.86 111.51
c3-c3-c3 gaff.datc3-J3-hc 46.34 109.80 c3-c3-hc
gaff.datc3-J3-SI 62.86 111.51 c3-c3-c3 gaff.datJ3-c3-hc 46.34
109.80 c3-c3-hc gaff.datJ3-SI-ha 47.78 109.50 J3-SI-ha
m1.itp GROMOS54A7, ATBSI-J3-hc 46.34 109.80 c3-c3-hc
gaff.dathc-J3-hc 39.40 107.58 hc-c3-hc gaff.datha-SI-ha 47.78
109.50 ha-SI-ha m1.itp GROMOS54A7, ATBDIHEc3-c3-J3-hc 1 0.16
0.0 3 hc-c3-c3-c3 gaff.datc3-c3-J3-SI 1 0.18 0.0 -3 c3-c3-c3-c3
gaff.datc3-c3-J3-SI 1 0.25 180.0 -2 c3-c3-c3-c3 gaff.datc3-c3-J3-SI
1 0.20 180.0 1 c3-c3-c3-c3 gaff.datc3-J3-SI-ha 1 1.415 0.0 3
c3-J3-SI-ha m1.itp GROMOS54A7, ATBhc-c3-J3-hc 1 0.15 0.0 3 hc-c3-c3-hc
gaff.dathc-c3-J3-SI 1 0.16 0.0 3 hc-c3-c3-c3 gaff.dathc-J3-SI-ha 9
1.40 0.0 3 X -c3-c3-X gaff.datIMPROPERNONBON J3 1.9080
0.1094 c3 gaff.dat SI 2.2200 0.3200
vdw_AMBER_parm99.defn*generated by hand:leap.in <
http://leap.in> - imposing
130 deg in SI--J3--hc anglesource leaprc.gaffaddAtomTypes { { "SI"
"Si" "sp3" } { "J3" "C" "sp3" } { "QS" "O" "sp3" } {
"QH" "O" "sp3" }}tes = loadmol2 m1.mol2loadamberparams m1.frcmodimpose tes
{ 1 } { { "SI" "CJ3" "H6" 130.0 } }saveamberparm tes tes130.prmtop
tes130.crdquitLog file: ./leap.logWelcome to LEaP!(no leaprc in search
path)Sourcing: ./leap.in <http://leap.in>----- Source:
/home/alechania/amber16/dat/leap/cmd/leaprc.gaff----- Source of
/home/alechania/amber16/dat/leap/cmd/leaprc.gaff doneLog file:
./leap.logLoading parameters:
/home/alechania/amber16/dat/leap/parm/gaff.datReading title:AMBER General
Force Field for organic molecules (Version 1.8, Mar 2015)Loading Mol2 file:
./m1.mol2Reading MOLECULE named M1Loading parameters: ./m1.frcmodReading
force field modification type file (frcmod)Reading title:remark goes
hereChecking Unit.Building topology.Building atom parameters.Building bond
parameters.Building angle parameters.Building proper torsion
parameters.Building improper torsion parameters. total 0 improper torsions
appliedBuilding H-Bond parameters.Incorporating Non-Bonded adjustments.Not
Marking per-residue atom chain types.Marking per-residue atom chain types.
(Residues lacking connect0/connect1 - these don't have chain types
marked: res total affected M1 1 ) (no restraints) Quitleap.in
<
http://leap.in> - imposing 90 deg in SI--J3--hc anglesource
leaprc.gaffaddAtomTypes { { "SI" "Si" "sp3" } { "J3" "C"
"sp3" } { "QS" "O" "sp3" } { "QH" "O" "sp3" }}tes = loadmol2
m1.mol2loadamberparams m1.frcmodimpose tes { 1 } { { "SI" "CJ3" "H6" 90.0 }
}saveamberparm tes tes90.prmtop tes90.crdquitlog:Welcome to LEaP!(no leaprc
in search path)Sourcing: ./leap2.in <http://leap2.in>----- Source:
/home/alechania/amber16/dat/leap/cmd/leaprc.gaff----- Source of
/home/alechania/amber16/dat/leap/cmd/leaprc.gaff doneLog file:
./leap.logLoading parameters:
/home/alechania/amber16/dat/leap/parm/gaff.datReading title:AMBER General
Force Field for organic molecules (Version 1.8, Mar 2015)Loading Mol2 file:
./m1.mol2Reading MOLECULE named M1Loading parameters: ./m1.frcmodReading
force field modification type file (frcmod)Reading title:remark goes
hereChecking Unit.Building topology.Building atom parameters.Building bond
parameters.Building angle parameters.Building proper torsion
parameters.Building improper torsion parameters. total 0 improper torsions
appliedBuilding H-Bond parameters.Incorporating Non-Bonded adjustments.Not
Marking per-residue atom chain types.Marking per-residue atom chain types.
(Residues lacking connect0/connect1 - these don't have chain types
marked: res total affected M1 1 ) (no restraints) Quit*search for
diference in generated structures:When trying to find differences between
files generated with different angles imposed:$ diff tes90.crd tes130.crd $
diff tes90.prmtop tes130.prmtop 1c1< %VERSION VERSION_STAMP = V0001.000
DATE = 07/03/18 08:42:53 ---> %VERSION VERSION_STAMP =
V0001.000 DATE = 07/03/18 08:42:49 No differences! Same happens
with the script generation of those structures: (see some differences in
inputs, but same results - none difference!)*generated by script (script
that worked for different parameters):leap.in <http://leap.in> :source
leaprc.gaffaddAtomTypes { { "SI" "Si" "sp3" } { "J3" "C"
"sp3" } { "QS" "O" "sp3" } { "QH" "O" "sp3" }}a12 = loadmol2
m1.mol2loadamberparams m1.frcmodimpose a12 {1}, { {"SI" "CJ3" "H6" 130}
}saveamberparm a12 a12.prmtop "amber_inps/a12_struc_39.mdcrd" quitLog file:
./leap.log>> #>> # ----- leaprc for loading the general Amber Force
field.>> # This file is mostly for use with Antechamber>> #>> # load
atom type hybridizations>> #>> addAtomTypes {>> { "h1" "H" "sp3" }>> {
"h2" "H" "sp3" }>> { "h3" "H" "sp3" }>> { "h4" "H" "sp3" }>> { "h5" "H"
"sp3" }>> { "ha" "H" "sp3" }>> { "hc" "H" "sp3" }>> { "hn" "H" "sp3" }>>
{ "ho" "H" "sp3" }>> { "hp" "H" "sp3" }>> { "hs" "H" "sp3" }>> { "hw"
"H" "sp3" }>> { "hx" "H" "sp3" }>> { "o" "O" "sp2" }>> { "o2" "O" "sp2"
}>> { "oh" "O" "sp3" }>> { "os" "O" "sp3" }>> { "ow" "O" "sp3" }>> { "c"
"C" "sp2" }>> { "c1" "C" "sp2" }>> { "c2" "C" "sp2" }>> { "c3" "C"
"sp3" }>> { "ca" "C" "sp2" }>> { "cc" "C" "sp2" }>> { "cd" "C" "sp2" }>>
{ "ce" "C" "sp2" }>> { "cf" "C" "sp2" }>> { "cg" "C" "sp2" }>> { "ch"
"C" "sp2" }>> { "cp" "C" "sp2" }>> { "cq" "C" "sp2" }>> { "cu" "C"
"sp2" }>> { "cv" "C" "sp2" }>> { "cx" "C" "sp2" }>> { "cy" "C" "sp2" }>>
{ "cz" "C" "sp2" }>> { "n" "N" "sp2" }>> { "n1" "N" "sp2" }>> { "n2"
"N" "sp2" }>> { "n3" "N" "sp3" }>> { "n4" "N" "sp3" }>> { "na" "N"
"sp2" }>> { "nb" "N" "sp2" }>> { "nc" "N" "sp2" }>> { "nd" "N" "sp2" }>>
{ "ne" "N" "sp2" }>> { "nf" "N" "sp2" }>> { "nh" "N" "sp2" }>> { "no"
"N" "sp2" }>> { "s" "S" "sp2" }>> { "s2" "S" "sp2" }>> { "s3" "S"
"sp3" }>> { "s4" "S" "sp3" }>> { "s6" "S" "sp3" }>> { "sh" "S" "sp3"
}>> { "ss" "S" "sp3" }>> { "sx" "S" "sp3" }>> { "sy" "S" "sp3" }>> {
"p2" "P" "sp2" }>> { "p3" "P" "sp3" }>> { "p4" "P" "sp3" }>> { "p5"
"P" "sp3" }>> { "pb" "P" "sp3" }>> { "pc" "P" "sp3" }>> { "pd" "P"
"sp3" }>> { "pe" "P" "sp3" }>> { "pf" "P" "sp3" }>> { "px" "P" "sp3"
}>> { "py" "P" "sp3" }>> { "f" "F" "sp3" }>> { "cl" "Cl" "sp3" }>> {
"br" "Br" "sp3" }>> { "i" "I" "sp3" }>> }>> #>> # Load the general force
field parameter set.>> #>> gaff = loadamberparams gaff.datLoading
parameters: /home/alechania/amber16/dat/leap/parm/gaff.datReading
title:AMBER General Force Field for organic molecules (Version 1.8, Mar
2015)> > addAtomTypes {> { "SI" "Si" "sp3" }> { "J3" "C"
"sp3" }> { "QS" "O" "sp3" }> { "QH" "O" "sp3" }> }> a12 =
loadmol2 m1.mol2Loading Mol2 file: ./m1.mol2Reading MOLECULE named M1>
loadamberparams m1.frcmodLoading parameters: ./m1.frcmodReading force field
modification type file (frcmod)Reading title:remark goes here> impose a12
{1}, { {"SI" "CJ3" "H6" 130} }> saveamberparm a12 a12.prmtop
"amber_inps/a12_struc_39.mdcrd" Checking Unit.Building topology.Building
atom parameters.Building bond parameters.Building angle parameters.Building
proper torsion parameters.Building improper torsion parameters. total 0
improper torsions appliedBuilding H-Bond parameters.Incorporating
Non-Bonded adjustments.Not Marking per-residue atom chain types.Marking
per-residue atom chain types. (Residues lacking connect0/connect1 -
these don't have chain types marked: res total affected M1 1 ) (no
restraints)> quit Quit*
--
Alechania Misturini
Mestranda em Físico-Química
Bacharel e Licenciada em Química
Grupo de Estrutura Eletrônica Molecular –〈
GE
⎜
EM
〉
*Departamento de Química – CFM*
*Universidade Federal de Santa Catarina – Brasil*
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Received on Tue Jul 03 2018 - 05:00:03 PDT
