Thank you.
First for the two single molecules, I did the following:
antechember to get the prepin file,
parmchk to get the frcmod file,
in tleap:
For the first molecule:
> mods=loadamberparams E2.frcmod
Loading parameters: ./E2.frcmod
Reading force field mod type file (frcmod)
> loadamberprep E2.prepin
Loading Prep file: ./E2.prepin
Loaded UNIT: BE2
> saveamberparm BE2 BE2.prmtop BE2.prmcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C13 H84 C16 C18
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C16 H88 C18 C19
** Warning: No sp2 improper torsion term for ca-oh-ca-ca
atoms are: C18 O20 C19 C17
** Warning: No sp2 improper torsion term for ca-ha-ca-ca
atoms are: C19 H86 C17 C15
old PREP-specified impropers:
<BE2 1>: C14 C13 C15 C17
<BE2 1>: C11 C15 C13 C16
<BE2 1>: C13 C18 C16 H84
<BE2 1>: C16 C19 C18 H88
<BE2 1>: C18 C17 C19 O20
<BE2 1>: C15 C19 C17 H86
total 2 improper torsions applied
6 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(no restraints)
> check BE2
Checking 'BE2'....
Checking parameters for unit 'BE2'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> saveoff BE2 BE2.off
Creating BE2.off
Saving BE2.
Building topology.
Building atom parameters.
> quit
Quit
For the second molecule:
> mods=loadamberparams MAA.frcmod
Loading parameters: ./MAA.frcmod
Reading force field mod type file (frcmod)
> loadamberprep MAA.prepin
Loading Prep file: ./MAA.prepin
Loaded UNIT: MAA
> saveamberparm MAA MAA.prmtop MAA.prmcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for c3-c2-ce-c
atoms are: C3 C4 C1 C2
** Warning: No sp2 improper torsion term for ce-ha-c2-ha
atoms are: C1 H18 C4 H20
old PREP-specified impropers:
<MAA 1>: C2 C4 C1 C3
<MAA 1>: C1 H20 C4 H18
<MAA 1>: C1 O5 C2 O6
total 1 improper torsion applied
3 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(no restraints)
> check MAA
Checking 'MAA'....
Checking parameters for unit 'MAA'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> saveoff MAA MAA.off
Creating MAA.off
Saving MAA.
Building topology.
Building atom parameters.
> mods=loadamberparams MAA.frcmod
Loading parameters: ./MAA.frcmod
Reading force field mod type file (frcmod)
> loadamberprep MAA.prepin
Loading Prep file: ./MAA.prepin
Loaded UNIT: MAA
> saveamberparm MAA MAA.prmtop MAA.prmcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for c3-c2-ce-c
atoms are: C3 C4 C1 C2
** Warning: No sp2 improper torsion term for ce-ha-c2-ha
atoms are: C1 H18 C4 H20
old PREP-specified impropers:
<MAA 1>: C2 C4 C1 C3
<MAA 1>: C1 H20 C4 H18
<MAA 1>: C1 O5 C2 O6
total 1 improper torsion applied
3 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(no restraints)
> check MAA
Checking 'MAA'....
Checking parameters for unit 'MAA'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> saveoff MAA MAA.off
Creating MAA.off
Saving MAA.
Building topology.
Building atom parameters.
> quit
Quit
For the complex (As it is not a "real" molecule, i use the frcmod and prepin
files from those single molecules, but load the pdb file of the complex):
> mods=loadamberparams E2.frcmod
Loading parameters: ./E2.frcmod
Reading force field mod type file (frcmod)
> mods2=loadamberparams MAA.frcmod
Loading parameters: ./MAA.frcmod
Reading force field mod type file (frcmod)
> loadamberprep E2.prepin
Loading Prep file: ./E2.prepin
Loaded UNIT: BE2
> loadamberprep MAA.prepin
Loading Prep file: ./MAA.prepin
Loaded UNIT: MAA
> mol=loadpdb complex.pdb
Loading PDB file: ./complex.pdb
Matching PDB residue names to LEaP variables.
(Residue 0: BE2, Terminal/beginning, was not found in name map.)
(Residue 1: MAA, Terminal/last, was not found in name map.)
ERROR: Comparing atoms
.R<BE2 1>.A<C17 43>,
.R<MAA 1>.A<H12 2>,
.R<MAA 1>.A<H14 3>, and
.R<MAA 1>.A<H16 4>
to atoms
.R<MAA 1>.A<C1 5>,
.R<BE2 1>.A<C17 43>,
.R<MAA 1>.A<H16 4>, and
.R<MAA 1>.A<H12 2>
This error may be due to faulty Connection atoms.
> mods=loadamberparams E2.frcmod
Loading parameters: ./E2.frcmod
Reading force field mod type file (frcmod)
> mods2=loadamberparams MAA.frcmod
Loading parameters: ./MAA.frcmod
Reading force field mod type file (frcmod)
> loadamberprep E2.prepin
Loading Prep file: ./E2.prepin
Loaded UNIT: BE2
> loadamberprep MAA.prepin
Loading Prep file: ./MAA.prepin
Loaded UNIT: MAA
> mol=loadpdb complex.pdb
Loading PDB file: ./complex.pdb
Matching PDB residue names to LEaP variables.
(Residue 0: BE2, Terminal/beginning, was not found in name map.)
(Residue 1: MAA, Terminal/last, was not found in name map.)
ERROR: Comparing atoms
.R<BE2 1>.A<C17 43>,
.R<MAA 1>.A<H12 2>,
.R<MAA 1>.A<H14 3>, and
.R<MAA 1>.A<H16 4>
to atoms
.R<MAA 1>.A<C1 5>,
.R<BE2 1>.A<C17 43>,
.R<MAA 1>.A<H16 4>, and
.R<MAA 1>.A<H12 2>
This error may be due to faulty Connection atoms.
In the terminal line, it shows:
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named C1 from MAA did not match !
!
!ABORTING.
Shuting
Quoting "David A. Case" <case.scripps.edu>:
> On Mon, May 30, 2005, gtg549i.mail.gatech.edu wrote:
>
> > Attachment are the files of pdb. mol1.pdb is the first molecule, mol2.pdb
> is
> > the second molecule, complex.pdb is the initial structure of complex of
> > molecule1 and molecule2.
>
> > > > 4.When i try to load it into xleap, the following messages come out:
> > > > !FATAL ERROR----------------------------------------
> > > > !FATAL: In file [chirality.c], line 142
> > > > !FATAL: Message: Atom named C1 from MAA did not match !
> > > > !
> > > > !ABORTING.
>
> I can't see any problems, using loadpdb to load complex.pdb into LEaP. Can
> you give the *exact* sequence of commands that you gave to encounter this
> error?
>
> Note that you have _very_ short distances between the two molecules: O5 of
> MAA
> and C10 of BE2 are only 1.6 Ang. apart. O5 of MAA and H74 of BE2 are only
> 1.3 Ang. apart. This should still not cause problems because you have a TER
> card between the systems, but you might see if the problem is related to
> having such a bad starting geometry.
>
> ...dac
>
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Received on Tue May 31 2005 - 20:53:01 PDT
