Ilyas,
That worked. Thank you.
Lili
On 9/7/07, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:
>
> Looks like you are missing some parameters. Use parmchk utility (AMBER 9
> pp 77) to create an frcmod file and load it to your leap script. 'parmchk'
> will create those missing parameters somehow. Good luck.
>
> On Fri, 7 Sep 2007, Lili Peng wrote:
>
> > Hi Ilyas,
> >
> > I specified Gaff as the force field as you described, and it resolved
> the
> > error...well, for the most part :). When I try to save the prmtop and
> > inpcrd files again, I get the error message:
> >
> > "Building bond parameters.
> > Could not find bond parameter for: c - h4
> > Building angle parameters.
> > Could not find angle parameter: c3 - c- h4
> > Could not find angle parameter: o - c - h4"
> >
> > where:
> > c-h4 refers to the C 11 -- HC 13 bond
> > c3-c-h4 refers to the CA 10 -- C 11 -- HC 13 angle
> > o-c-h4 refers to the O 12 -- C 11 -- HC 13 angle
> >
> > The other atom types in this file are: o c, c3, hc, h1, hn, n, and n3
> > (this information was obtained from an error message when I did not
> specify
> > Gaff as the force field)
> >
> > So something went wrong in the parameterization for these bonds and
> angles?
> > I double checked these bonds and angles in Accelrys DS, and they seemed
> > fine. The interesting thing is that this error has to do something with
> the
> > hydrogen h4 atom - maybe it wasn't parameterized accurately? Is there a
> way
> > for xleap to add the hydrogen automatically to a prepi file?
> >
> > I encountered no errors in building the topology, angles, proper
> torsions,
> > and improper torsions.
> >
> > Lili
> >
> > On 9/7/07, Ilyas Yildirim <yildirim.pas.rochester.edu > wrote:
> > >
> > > Lili,
> > >
> > > Add 'source leaprc.gaff' to your xleap.in input script. Because you
> > > created the modified residue using antechamber (I assume you used the
> atom
> > >
> > > type gaff in antechamber), you need to load gaff force field
> parameters.
> > > Hope this works.
> > >
> > > Best,
> > >
> > > On Fri, 7 Sep 2007, Lili Peng wrote:
> > >
> > > > Hi Junmei and Dr. Case,
> > > >
> > > > Junmei - I ran your commands and they worked smoothly. However, now
> my
> > > > challenge is to generating the parameter and topology files (seems
> like
> > > once
> > > > I overcome an obstacle another one appears?!). I ran the following
> > > commands
> > > > in xleap:
> > > >
> > > > 1. tleap: loadamberprep glu3.prepi
> > > > 2. tleap: edit GLU
> > > > (new box with the glu3 structure pops up - the structure looks
> > > okay).
> > > > 3. xleap: I select all and relax the structure.
> > > > 4. tleap: solvatebox GLU TIP3PBOX 10
> > > > (...823 residues added successfully)
> > > > 5. tleap: saveamberparm GLU glu3.prmtop glu3.inpcrd
> > > > ...and this is where I get the error message:
> > > >
> > > > Checking Unit.
> > > > Building topology.
> > > > Building atom parameters.
> > > > For atom: .R<GLU 1>.A <OE1 1> Could not find type: o
> > > > For atom: .R<GLU 1>.A <CD 2> Could not find type: c
> > > > For atom: .R<GLU 1>.A <OE2 3> Could not find type: o
> > > > For atom: .R<GLU 1>.A <CG 4> Could not find type: c3
> > > > ...etc.
> > > > The error encompasses all 32 atoms from OE1 to O30.
> > > >
> > > > Is this a problem with assigning atom types in antechamber? I
> thought
> > > that
> > > > by running antechamber, the features of atomtype would be already
> > > included?
> > > > A similar problem to mine is discussed in this thread (
> > > > http://archive.ambermd.org/200609/0059.html
> > > and
> > > > the authors state that a modified force field (frcmod) file is
> > > missing. Am
> > > > I missing force field parameters? I'm running xleap in the
> > > > leaprc.ff99SBforce field.
> > > >
> > > > I know you're probably really busy right now, so thanks for your
> > > patience
> > > > and help as I muscle through this problem.
> > > >
> > > > Thanks,
> > > > Lili
> > > >
> > > > On 9/6/07, Junmei Wang <junmwang.yahoo.com> wrote:
> > > > >
> > > > > Hi, Lili,
> > > > > I don't know why the mol2 format does not work for this molecule.
> But
> > > the
> > > > > xleap works fine for the prepi format. Please run the following
> > > commands:
> > > > >
> > > > > 1 antechamber -fi pdb -fo mol2 -i glu3_orig.pdb -o glu3.mol2
> > > > > 2 manually delete the bond between O30 and O32 in
> > > ANTECHAMBER_BOND_TYPE.AC
> > > > > 3 antechamber -fi ac -fo prepi -i ANTECHAMBER_BOND_TYPE.AC -o
> > > glu3.prepi
> > > > > 4 start xleap
> > > > > 5 loadamberprep glu3.prepi
> > > > > 6 edit GLU
> > > > >
> > > > > Good luck
> > > > >
> > > > > Junmei
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > *Lili Peng <lilipeng.gmail.com >* wrote:
> > > > >
> > > > > Hi Junmei,
> > > > >
> > > > > Thanks for your help. I converted my original pdb file into mol2
> > > format
> > > > > using the exact command you prescribed (using ANTECHAMBER_AC.AC
> and
> > > all),
> > > > > and that worked just fine. However, now I want to load the file
> into
> > > xLeap,
> > > > > and I try the commend "x = loadmol2 glu3.mol2" and then tried to
> view
> > > the
> > > > > structure using "edit x" but xLeap only opens an empty box. Now
> I'm
> > > back at
> > > > > square one (see my thread
> > > http://amber.ch.ic.ac.uk/archive/200708/0330.html
> > > > > ), stuck at figuring how to load a mol2 file into xleap. David
> Case
> > > > > previously suggested that I convert it into pdb format, so I tried
> two
> > >
> > > > > things:
> > > > >
> > > > > 1) I converting my new mol2 file BACK into pdb using the command
> > > > > "/antechamber -i glu3.mol2 -fi mol2 -o glu3.pdb -fo pdb -j 0". But
> > > when I
> > > > > loaded the new pdb file into xleap, I get the error "the file
> > > contained 5
> > > > > atoms not in residue templates."
> > > > > 2) I used my original pdb file. But when I loaded into xleap, I
> > > receive
> > > > > the same error of atoms not being in residue templates.
> > > > >
> > > > > Basically I am stuck on how to obtain the proper PDB file for this
> > > > > structure ( is it always this hard?!).
> > > > >
> > > > > I have attached my original pdb, new pdb, and mol2 files for your
> > > > > convenience. Please advise on what I should do.
> > > > >
> > > > > Thanks and regards,
> > > > > Lili
> > > > >
> > > > > On 8/31/07, Junmei Wang < junmwang.yahoo.com > wrote:
> > > > > >
> > > > > > I took a look at the attached pdb file and found the structure
> is
> > > not
> > > > > > good enough. Since no bond connectivity information is read in
> for a
> > > pdb
> > > > > > format, antechamber tries to predict the bond connectivity table
> > > itself
> > > > > > based on the atomic distances. If the input structure is not
> good
> > > enough,
> > > > > > errors may happen. For your molecule, the distance between O30
> and
> > > O32 is
> > > > > > too small and antechamber wrongly assumes there is a bond there.
> > > This is my
> > > > > > suggestion:
> > > > > >
> > > > > > (1) Try to use mol2 or sdf files as input
> > > > > > (2) If you really want to use pdb format, try "-j 0" flag to
> check
> > > > > > unexpected bond connectivity in ANTECHAMBER_AC.AC if error
> happens.
> > > > > > Command: antechamber -fi pdb -fo mol2 -i gau3.pdb -o gau3.mol2-j 0
> > > > > >
> > > > > > For you molecule, you will find a bond is formed between O30 and
> > > O32.
> > > > > >
> > > > > > Then manually delete that bond and read ANTECHAMBER_AC.AC as
> input
> > > (ac
> > > > > > format)
> > > > > >
> > > > > > Command: antechamber -fi ac -fo mol2 -i ANTECHAMBER_AC.AC -o
> > > gau3.mol2
> > > > > >
> > > > > > Good luck
> > > > > >
> > > > > > Junmei
> > > > > >
> > > > > >
> > > > > > run antechamber with "-j 0" and check ANTECHAMBER_AC.AC file to
> find
> > > > > > unexpected bond connection
> > > > > > antechamber -fi pdb -fo mol2 -i input.pdb -o input.mol2 -j 0
> > > > > >
> > > > > >
> > > > > > *Lili Peng <lilipeng.gmail.com >* wrote:
> > > > > >
> > > > > > Hi Dr. Case,
> > > > > >
> > > > > > Okay, I added the hydrogens to get the PDB file:
> > > > > >
> > > > > > REMARK Accelrys Discovery Studio PDB file
> > > > > >
> > > > > > REMARK Created: Thu Aug 30 13:40:47 Pacific Daylight Time
> 2007
> > > > > > ATOM 1 N GLU 1 3.326 1.548 -0.000 1.00
> 0.00
> > > > > > N ATOM 2 CA GLU 1 3.970 2.846 -0.000
> 1.00
> > > 0.00
> > > > > > C ATOM 3 CB GLU 1 3.577 3.654 1.232
> 1.00
> > > 0.00
> > > > > > C ATOM 4 CG GLU 1 4.267 4.996 1.195
> 1.00
> > > > > > 0.00 C ATOM 5 CD GLU 1 3.874
> 5.805
> > > > > > 2.429 1.00 0.00 C ATOM 6 OE1 GLU 1
> > > > > > 4.595 5.679 3.454 1.00 0.00 O
> ATOM 7 OE2
> > > GLU
> > > > > > 1 2.856 6.542 2.334 1.00 0.00 O
> > > ATOM 8 C
> > > > > > GLU 1 5.486 2.705 -0.000 1.00 0.00 C
> > > ATOM
> > > > > > 9 O GLU 1 6.009 1.593 -0.000 1.00 0.00
> > > O
> > > > > > ATOM 10 C18 GLU 1 1.933 1.409 -0.374 1.00
> 0.00
> > > > > > C ATOM 11 O20 GLU 1 2.167 0.156 -0.632
> 1.00
> > > 0.00
> > > > > > O ATOM 12 C22 GLU 1 0.785 1.600 -1.382
> 1.00
> > > 0.00
> > > > > > C ATOM 13 C23 GLU 1 - 0.602 0.995 -1.094
> 1.00
> > > > > > 0.00 C ATOM 14 C24 GLU 1 -1.750
> 1.187
> > > -
> > > > > > 2.103 1.00 0.00 C ATOM 15 C25 GLU
> 1 -
> > > 3.136
> > > > > > 0.582 -1.815 1.00 0.00 C ATOM 16 O30 GLU
> > > 1
> > > > > > -4.020 1.377 -2.341 1.00 0.00 O ATOM
> 17 O32
> > > GLU
> > > > > > 1 -3.796 -0.414 -1.923 1.00 0.00 O ATOM
> > > 18 N34
> > > > > > GLU 1 -1.877 2.648 -2.420 1.00 0.00
> > > N ATOM
> > > > > > 19 HT GLU 1 3.887 0.681 0.280 1.00 0.00
> > > H ATOM
> > > > > > 20 HA GLU 1 3.642 3.359 -0.904 1.00 0.00
> > > > > > H ATOM 21 HB1 GLU 1 2.497 3.801 1.241
> 1.00
> > > > > > 0.00 H ATOM 22 HB2 GLU 1 3.878
> 3.116
> > > > > > 2.131 1.00 0.00 H ATOM 23 HG1 GLU 1
> > > 5.347
> > > > > > 4.849 1.186 1.00 0.00 H ATOM 24 HG2
> GLU 1
> > > > > > 3.966 5.535 0.297 1.00 0.00 H ATOM
> > > 25 HC GLU
> > > > > > 1 6.112 3.597 -0.000 1.00 0.00 H ATOM
> > > 26
> > > > > > 1H22 GLU 1 0.642 2.675 -1.495 1.00 0.00
> H
> > > > > > ATOM 27 2H22 GLU 1 1.123 1.177 -2.328 1.00
> 0.00
> > > > > > H ATOM 28 1H23 GLU 1 -0.459 -0.079 -0.981
> 1.00
> > > 0.00
> > > > > > H ATOM 29 2H23 GLU 1 -0.940 1.419 -0.149
> 1.00
> > > 0.00
> > > > > > H ATOM 30 H24 GLU 1 - 1.429 0.576 -2.946
> 1.00
> > > > > > 0.00 H ATOM 31 1H34 GLU 1 -0.960
> 3.003
> > > -
> > > > > > 2.843 1.00 0.00 H ATOM 32 2H34 GLU
> 1 -
> > > 2.089
> > > > > > 3.191 -1.522 1.00 0.00 H TER 33 GLU
> > > 1
> > > > > >
> > > > > >
> > > > > >
> > > > > > END
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > Still, when I try to run the command " antechamber -fi pdb -i
> > > glu3.pdb-fo mol2 -o
> > > > > > glu3.mol2" in Amber, I get the same old error message
> > > > > >
> > > > > > "Warning: the assigned bond types may be wrong...
> > > > > >
> > > > > > Error: cannot run "usr/local/apps/amber9/exe/bondtype -i
> > > > > > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j
> full"
> > > in
> > > > > > judgebondtype() of antechamber.c properly, exit"
> > > > > >
> > > > > > I double checked the bond types of each atom, and I don't see
> any
> > > > > > errors. What am I doing wrong now? I have attached my updated
> PDB
> > > file for
> > > > > > your convenience.
> > > > > >
> > > > > > Thanks,
> > > > > > Lili
> > > > > >
> > > > > > On 8/27/07, David A. Case < case.scripps.edu > wrote:
> > > > > > >
> > > > > > > On Mon, Aug 27, 2007, Lili Peng wrote:
> > > > > > > >
> > > > > > > > Thanks for your reply. I tried running antechamber
> initially
> > > (as
> > > > > > > you
> > > > > > > > prescribed), but my converted mol2 file is really
> weird. The
> > > carbon
> > > > > > > atoms
> > > > > > > > get converted to Californium and Cerium atoms. There's even
> a
> > > Neon
> > > > > > > atom in
> > > > > > > > the structure, as well as many "Unknowns". I have no idea
> how
> > > the
> > > > > > > carbon
> > > > > > > > atoms got converted into them.
> > > > > > >
> > > > > > > Here is the "glu3.pdb" file:
> > > > > > > REMARK Accelrys Discovery Studio PDB file
> > > > > > > REMARK Created: Mon Aug 27 13:56:43 Pacific Daylight Time
> 2007
> > > > > > > ATOM 1 N GLU 1 3.326 1.548 -0.000 1.00
> 0.00
> > > > > > > N
> > > > > > > ATOM 2 CA GLU 1 3.970 2.846 -0.000 1.00
> 0.00
> > > > > > > C
> > > > > > > ATOM 3 CB GLU 1 3.577 3.654 1.232 1.00
> 0.00
> > > > > > > C
> > > > > > > ATOM 4 CG GLU 1 4.267 4.996 1.195 1.00
> 0.00
> > > > > > > C
> > > > > > > ATOM 5 CD GLU 1 3.874 5.805 2.429 1.00
> 0.00
> > > > > > > C
> > > > > > > ATOM 6 OE1 GLU 1 4.595 5.679 3.454 1.00
> 0.00
> > > > > > > O
> > > > > > > ATOM 7 OE2 GLU 1 2.856 6.542 2.334 1.00
> 0.00
> > > > > > > O
> > > > > > > ATOM 8 C GLU 1 5.486 2.705 -0.000 1.00
> 0.00
> > > > > > > C
> > > > > > > ATOM 9 O GLU 1 6.009 1.593 -0.000 1.00
> 0.00
> > > > > > > O
> > > > > > > TER 10 GLU 1
> > > > > > > HETATM 11 C A 1 - 1.198 -0.215 0.736 1.00
> > > 0.00
> > > > > > > C
> > > > > > > HETATM 12 C A 1 0.108 0.559 0.560 1.00
> 0.00
> > > > > > > C
> > > > > > > HETATM 13 C A 1 1.275 -0.423 0.476 1.00
> > > 0.00
> > > > > > > C
> > > > > > > HETATM 14 C A 1 2.565 0.342 0.301 1.00
> 0.00
> > > > > > > C
> > > > > > > HETATM 15 O A 1 3.623 -0.259 0.212 1.00
> 0.00
> > > > > > > O
> > > > > > > HETATM 16 N A 1 - 1.398 -1.128 -0.431 1.00
> > > 0.00
> > > > > > > N
> > > > > > > HETATM 17 C A 1 - 2.351 0.756 0.820 1.00
> > > 0.00
> > > > > > > C
> > > > > > > HETATM 18 O A 1 -3.054 0.784 1.816 1.00
> 0.00
> > > > > > > O
> > > > > > > HETATM 19 O A 1 - 2.590 1.543 -0.148 1.00
> > > 0.00 O
> > > > > > > TER 20 A 1
> > > > > > > END
> > > > > > >
> > > > > > > Antechamber is limited in the types of pdb files it can
> handle:
> > > > > > >
> > > > > > >
> > > > > > > 1. Every atom in a residue needs to have a unique atom
> name. You
> > > have
> > > > > > > five
> > > > > > > atoms all named "C". (Actually, antechamber takes care of
> this,
> > > but
> > > > > > > other
> > > > > > > parts of amber will not, so it is a good idea to make sure of
> it
> > > by
> > > > > > > hand.)
> > > > > > >
> > > > > > > 2. The input pdb file must have all atoms present, *including
> > > > > > > hydrogens.*
> > > > > > > This is where you really go wrong, since there are no hydrogen
> > > atoms
> > > > > > > present
> > > > > > > in your input file. See if discovery studio can put these on,
> or
> > > > > > > build them
> > > > > > > by hand in xleap, or in some other modeling program.
> > > > > > >
> > > > > > > 3. The things you think are Californium, neon, etc, are
> really
> > > atom
> > > > > > > types,
> > > > > > > not elements. Given that it had no hydrogens, antechamber
> tried
> > > to
> > > > > > > make
> > > > > > > multiple bonds between lots of things, and the quantum
> > > optimization
> > > > > > > was of
> > > > > > > course very weird.
> > > > > > >
> > > > > > > So: edit the names in the pdb file, and get some hydrogens on
> > > there!
> > > > > > >
> > > > > > > ...good luck...dac
> > > > > > >
> > > > > > > ------------------------------------------------------------
> > > > > > > -----------
> > > > > > > The AMBER Mail Reflector
> > > > > > > To post, send mail to amber.scripps.edu
> > > > > > > To unsubscribe, send "unsubscribe amber" to
> majordomo.scripps.edu
> > > > > > >
> > > > > >
> > > > > >
> > > > > > ------------------------------
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> > > > > > <
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> > > >,
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> > > > >
> > > > >
> > > >
> > >
> > > --
> > > Ilyas Yildirim
> > > ---------------------------------------------------------------
> > > = Department of Chemistry - =
> > > = University of Rochester - =
> > > = Hutchison Hall, # B10 - =
> > > = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> > > = http://www.pas.rochester.edu/~yildirim/<
> http://www.pas.rochester.edu/%7Eyildirim/>
> > > =
> > > ---------------------------------------------------------------
> > >
> > >
> -----------------------------------------------------------------------
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> > >
> >
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> = Department of Chemistry - =
> = University of Rochester - =
> = Hutchison Hall, # B10 - =
> = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> = http://www.pas.rochester.edu/~yildirim/ =
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
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Received on Sun Sep 09 2007 - 06:07:49 PDT
