Re: AMBER: Prepin error (?) in xleap

From: Lili Peng <lilipeng.gmail.com>
Date: Thu, 6 Sep 2007 15:32:48 -0700

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
> >
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>
>
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Received on Sun Sep 09 2007 - 06:07:23 PDT
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