AMBER Archive (2007)

Subject: Re: AMBER: Prepin error (?) in xleap

From: Lili Peng (lilipeng_at_gmail.com)
Date: Fri Sep 07 2007 - 16:54:23 CDT

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://structbio.vanderbilt.edu/archives/amber-archive/2006/2678.php), 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_at_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_at_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_at_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_at_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_at_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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