Thanks for advice. Creating the mol2 file using antechamber helped so
I got the frcmod files.So in the next step I wanted do generate the
prmtop and inpcrd files and get the following error:
Checking Unit.
WARNING: There is a bond of 4.899159 angstroms between:
------- .R<ATU 720>.A<C10 17> and .R<ATU 720>.A<C11 20>
WARNING: There is a bond of 4.592322 angstroms between:
------- .R<ATU 720>.A<C7 12> and .R<ATU 720>.A<C12 22>
WARNING: There is a bond of 4.602933 angstroms between:
------- .R<ATU 720>.A<C3 7> and .R<ATU 720>.A<C4 8>
WARNING: There is a bond of 4.622260 angstroms between:
------- .R<ATU 720>.A<C 2> and .R<ATU 720>.A<C1 5>
WARNING: There is a bond of 4.885310 angstroms between:
------- .R<ATU 721>.A<C10 17> and .R<ATU 721>.A<C11 20>
WARNING: There is a bond of 4.617752 angstroms between:
------- .R<ATU 721>.A<C7 12> and .R<ATU 721>.A<C12 22>
WARNING: There is a bond of 4.612683 angstroms between:
------- .R<ATU 721>.A<C3 7> and .R<ATU 721>.A<C4 8>
WARNING: There is a bond of 3.533443 angstroms between:
------- .R<ATU 721>.A<C 2> and .R<ATU 721>.A<C1 5>
WARNING: The unperturbed charge of the unit: 15.002000 is not zero.
FATAL: Atom .R<ATU 720>.A<O22 34> does not have a type.
FATAL: Atom .R<ATU 720>.A<N20 35> does not have a type.
FATAL: Atom .R<ATU 720>.A<O21 36> does not have a type.
FATAL: Atom .R<ATU 720>.A<C18 37> does not have a type.
FATAL: Atom .R<ATU 720>.A<C19 38> does not have a type.
FATAL: Atom .R<ATU 720>.A<C16 39> does not have a type.
FATAL: Atom .R<ATU 720>.A<C17 40> does not have a type.
FATAL: Atom .R<ATU 720>.A<N11 41> does not have a type.
FATAL: Atom .R<ATU 720>.A<O4 42> does not have a type.
FATAL: Atom .R<ATU 721>.A<O22 34> does not have a type.
FATAL: Atom .R<ATU 721>.A<N20 35> does not have a type.
FATAL: Atom .R<ATU 721>.A<O21 36> does not have a type.
FATAL: Atom .R<ATU 721>.A<C18 37> does not have a type.
FATAL: Atom .R<ATU 721>.A<C19 38> does not have a type.
FATAL: Atom .R<ATU 721>.A<C16 39> does not have a type.
FATAL: Atom .R<ATU 721>.A<C17 40> does not have a type.
FATAL: Atom .R<ATU 721>.A<N11 41> does not have a type.
FATAL: Atom .R<ATU 721>.A<O4 42> does not have a type.
Failed to generate parameters
So this is what I did:
1.Creating the atu.lib (because ATU is the name of the ligand in the
complex)
source leaprc.ff99SB
source leaprc.gaff
ATU = loadmol2 paullon.mol2
check ATU
loadamberparams paullon.frcmod
saveoff ATU atu.lib
saveamberparm ATU paullon.prmtop paullon.inpcrd
quit
2.Creating the prmtop/inpcrd files of the complex:
source leaprc.ff99SB
source leaprc.gaff
loadamberparams paullon.frcmod
loadoff atu.lib
complex = loadpdb 1q3w.pdb
saveamberparm complex 1q3w.prmtop 1q3w.inpcrd (this is where I got the
error)
savepdb complex 1q3w_atu.pdb
quit
Sry if I bother you.
Bernhard
Zitat von Dmitry Nilov <nilovdm.gmail.com>:
> Input mol2 file for parmchk usually includes Amber atom types. It
> seems that you got your mol2 fil not with the use of antechamber,
> thus
> it contains unknown atom types such as "C.ar" for example. Try to
> use
> antechamber to create mol2. Note that both antechamber and parmchk
> could look for parameters (atom types, force constants, etc.) in
> various force fields (GAFF, ff99SB, etc., default is GAFF), see
> the
> program options in manual.
>
> On Wed, Jan 26, 2011 at 12:49 PM, <poll.chemie.uni-hamburg.de>
> wrote:
> > Hi everybody,
> >
> > I'm pretty new to AMBER. Yesterday I tried the antechamber
> tutorial
> > which worked fine with the given example. So wanted to do this
> again
> > with some other molecule (attached). It pretty much works until
> I
> > want to use the parmchk command to get the frcmod-file. Then I
> get an
> > infinite loop in the frcmod-file lookin' like this:
> >
> > MASS
> > N.am 0.000 0.000 ATTN, need revision
> > H 1.008 0.161 same as hn
> > C.2 0.000 0.000 ATTN, need revision
> > C.3 0.000 0.000 ATTN, need revision
> > C.ar 0.000 0.000 ATTN, need revision
> > N.pl3 0.000 0.000 ATTN, need revision
> > O.2 0.000 0.000 ATTN, need revision
> >
> > BOND
> > N.am-H 0.00 0.000 ATTN, need revision
> > N.am-C.2 0.00 0.000 ATTN, need revision
> > C.2-C.3 0.00 0.000 ATTN, need revision
> > C.2-O.2 0.00 0.000 ATTN, need revision
> > C.3-H 0.00 0.000 ATTN, need revision
> > -N.pl3 0.00 0.000 ATTN, need revision
> > N.am-H 0.00 0.000 ATTN, need revision
> > -N.pl3 0.00 0.000 ATTN, need revision
> > N.am-H 0.00 0.000 ATTN, need revision
> > -N.pl3 0.00 0.000 ATTN, need revision
> > N.am-H 0.00 0.000 ATTN, need revision
> > -N.pl3 0.00 0.000 ATTN, need revision
> > N.am-H 0.00 0.000 ATTN, need revision
> > -N.pl3 0.00 0.000 ATTN, need revision
> >
> > So I checked the atom types in SYBYL and checked the mol2 file
> using
> > acdoctor. This invastigations told me everything is fine and
> there
> > should be no problem. Maybe some of you finds the mistake(s).
> >
> > Thanks in advance
> >
> > Bernhard
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
> --
> Dmitry Nilov,
> Lomonosov Moscow State University
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 26 2011 - 08:30:02 PST
