Hi,
I'm not sure what's causing the behavior you are seeing, but an
alternative to LEaP's 'impose' command (at least for dihedrals) is the
'rotatedihedral' command of cpptraj. It uses either conventional
torsion names (e.g. phi, psi, etc) or atom masks. For example,
parm ../tz2.parm7
loadcrd ../tz2.nc 1 1 name TZ2
rotatedihedral crdset TZ2 value 35 res 8 type chip
crdout TZ2 tz2.rotate.1.mol2
Will rotate the chi angle in residue 8 (here 'chip' means "chi
protein" to distinguish it from 'chin', "chi nucelotide") to a value
of 35 degrees.
parm ../tz2.parm7
loadcrd ../tz2.nc 1 1 name TZ2
rotatedihedral crdset TZ2 increment -19.3 :8.N :
8.CA :8.CB :
8.CG
crdout TZ2 tz2.rotate.2.mol2
Will rotate the torsion formed by atoms N, CA, CB, and CG in residue 8
by -19.3 degrees.
In both cases a mol2 is being written out, but you can of course write
out in any format cpptraj understands. See the manual for more
details.
-Dan
On Tue, Jul 3, 2018 at 7:57 AM, Alechania Misturini
<alechaniam.gmail.com> wrote:
> 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:
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> **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*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jul 03 2018 - 06:00:03 PDT
