Hello Amber users!
I am having pretty much the same problem that Lili has, I was just
wondering what does it mean a message:
For atom[2323]:OG, the best APS is not zero, exit
For atom[2324]:OG, the best APS is not zero, exit
Respect
Eduardo
Junmei Wang 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
> <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
> <mailto: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 <mailto: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
> <mailto: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
>
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Received on Sun Sep 09 2007 - 06:07:27 PDT
