AMBER Archive (2007)

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

From: Lili Peng (lilipeng_at_gmail.com)
Date: Fri Sep 07 2007 - 16:22:42 CDT

Hi Eduardo,

I've asked this question before - check it out and Dr. Case's reply in this
thread: http://structbio.vanderbilt.edu/archives/amber-archive/2007/3073.php

A good idea is to always Google the problem - chances are someone has run
into the same problem and asked it on the mailing list. As stated in the
AMBER tutorials, "Google is your friend."

Regards,
Lili

On 9/6/07, Eduardo Mendez <pckboy_at_gmail.com> wrote:
>
> 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_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
> > <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
> > <mailto: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 <mailto: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
> > <mailto: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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