[gmx-users] pdb2gmx problems and modified AA's

Dr Seth Carlton OLSEN s.olsen1 at uq.edu.au
Sat Oct 9 11:29:18 CEST 2004


Hi Gromacs Users,

Regarding the warning below that atom 'O2' is missing from the pdb, does this relate to the fact that atom 'O' was removed during the workings of pdb2gmx?  If 'O' was removed (the program said it was redundant) and 'O2' was named 'O' this would be consistent with the warning.  Is this what's happening?  Why does pdb2gmx not want to take the name 'O2', and why does it appear to rename the atom in conflict with another and then delete one of the pair it then believes is redundant?

Cheers,

Seth



Hi Gromacs Users,

Thanks David for that point.  I have renamed NE1 to NE3 (since there is also a CE2) in the rtp, hdb files and in the pdb I'm trying to process.  The fatal error then read:

Fatal error: Atom HE31 not found in rtp database in residue CRQ, it looks a bit like HE11

Accordingly, I changed the nitrogen-bonded hydrogen atoms (there should be 2) to HE31 and HE32 respectively.  However, this generated the following fatal errors:

WARNING: atom HD11 is missing in residue CRQ 62 in the pdb file
         You might need to add atom HD11 to the hydrogen database of residue CRQ         in the file ff???.hdb (see the manual)
 
 
WARNING: atom HE11 is missing in residue CRQ 62 in the pdb file
         You might need to add atom HE11 to the hydrogen database of residue CRQ         in the file ff???.hdb (see the manual)
 
 
WARNING: atom HE21 is missing in residue CRQ 62 in the pdb file
         You might need to add atom HE21 to the hydrogen database of residue CRQ         in the file ff???.hdb (see the manual)
 
 
WARNING: atom HD21 is missing in residue CRQ 62 in the pdb file
         You might need to add atom HD21 to the hydrogen database of residue CRQ         in the file ff???.hdb (see the manual)
 
 
WARNING: atom HB21 is missing in residue CRQ 62 in the pdb file
         You might need to add atom HB21 to the hydrogen database of residue CRQ         in the file ff???.hdb (see the manual)
 
 
WARNING: atom O2 is missing in residue CRQ 62 in the pdb file

Fatal error: There were 6 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing

I have added the requisite lines to the hbd file, so I'm not sure why it does not find them.  The hydrogens are not in the pdb file - I am adding them through the use of pdb2gmx.  I'm not sure why it states that 02 is not in the pdb, since it is definitely there.  Does pdb2gmx expect to find the hydrogens in the pdb file? 

Cheers,

Seth

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Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au

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----- Original Message -----
From: David <spoel at xray.bmc.uu.se>
Date: Saturday, October 9, 2004 6:37 pm
Subject: Re: [gmx-users] pdb2gmx problems and modified AA's

> On Sat, 2004-10-09 at 10:05, Dr Seth Carlton OLSEN wrote:
> > Hi Gromacs Users,
> >
> > I am trying to run a pdb through pdb2gmx to get files to do an md
> run.  The protein chain contains an unconventional residue ('CRQ',
> in the pdb).  I am using the OPLS-AA forcefield.  I have modified
> the ffoplsaa.rtp, ffoplsaa.hdb and aminoacids.dat files by adding
> the following sections:
> > **added to ffoplsaa.rtp
> > ;CRQ - chromophore GYQ from Rtms5 structure
> > [CRQ]
> >  [ atoms ]
> >     CD1    opls_145    0.029     1
> >    HD11    opls_146    0.000     1
> >     CE1    opls_145    0.030     1
> >    HE11    opls_146    0.000     1
> >     CZ     opls_166    0.204     1
> >     OH     opls_167   -1.316     1
> >     CE2    opls_145    0.029     1
> >    HE21    opls_146    0.000     1
> >     CD2    opls_145    0.029     1
> >    HD21    opls_146    0.000     1
> >     CG2    opls_145    0.050     1
> >     CB2    opls_142    0.064     1
> >    HB21    opls_144    0.000     1
> >     CA2    opls_141    0.204     1
> >     N2     opls_559   -0.436     1
> >     C2     opls_235    0.340     1
> >     O2     opls_236   -0.632     1
> >     N3     opls_557    0.110     1
> >     CA3    opls_223    0.134     1
> >    HA31    opls_140    0.000     1
> >    HA32    opls_140    0.000     1
> >     C      opls_235    0.433     1
> >     O      opls_236   -1.316     1
> >     C1     opls_558    0.340     1
> >     CA1    opls_257    0.204     1
> >     N      opls_251   -0.838     1
> >     CB1    opls_136    0.133     1
> >    HB11    opls_140    0.000     1
> >    HB12    opls_140    0.000     1
> >     CG1    opls_136    0.133     1
> >    HG11    opls_140    0.000     1
> >    HG12    opls_140    0.000     1
> >     CD3    opls_139    0.433     1
> >     OE1    opls_235   -0.632     1
> >     NE1    opls_237    0.127     1
> >     HAE    opls_909    0.072     1
> >     HAD    opls_909    0.072     1
> >  [ bonds ]                                
> >    CD1   CE1
> >    CD1  HD11
> >    CD1   CG2
> >    CE1    CZ
> >    CE1  HE11
> >     CZ    OH
> >     CZ   CE2
> >    CE2   CD2
> >    CE2  HE21
> >    CD2   CG2
> >    CD2  HD21
> >    CG2   CB2
> >    CB2   CA2
> >    CB2  HB21
> >    CA2    N2
> >    CA2    C2
> >     N2    C1
> >     C2    O2
> >     C2    N3
> >     N3   CA3
> >     N3    C1
> >    CA3     C
> >    CA3  HA31
> >    CA3  HA32
> >      C     O
> >     C1   CA1
> >    CA1     N
> >    CA1   CB1
> >    CB1   CG1
> >    CB1  HB11
> >    CB1  HB12
> >    CG1   CD3
> >    CG1  HG11
> >    CG1  HG12
> >    CD3   OE1
> >    CD3   NE1
> >    NE1   HAE
> >    NE1   HAD
> >     -C     N
> > [ impropers ]
> >     CA    +N     C     O    improper_O_C_X_Y
> >
> > ***added to ffoplsaa.hdb
> > CRQ     9
> >  1 1 CD1 CE1 CG2
> >  1 1 CE1 OH CD1
> >  1 1 CD2 CE2 CG2
> >  1 1 CE2 OH CD2
> >  1 1 CB2 CG2 CA2
> >  2 6 CB1 CA1 CG1
> >  2 6 CG1 CB1 CD3
> >  2 3 NE1 CD3 OE1
> >  2 6 CA3 N3 C
> >
> > ***added to aminoacids.dat
> > CRQ
> >
> >
> > when I run pdb2gmx on the pdb file 'pdb1mou.ent' (too large to be
> included here) I get the following error, which kills pdb2gmx:
> > Fatal error: Atom HE12 not found in rtp database in residue CRQ,
> it looks a bit like HE11
> >
> pdb2gmx makes hydrogens by modifying the name of the atom it is bound
> to. In your case you have NE1, so it wants to make HE12 and HE11. You
> have however also a CE1. I would recommend to rename NE1 to NE2 and
> thehydrogens to HE21 and HE22.
>
> Did you also modify the ffoplsaa.hdb file?
>
> > However, I am not sure why pdb2gmx is looking for this atom. 
> HE12 is not included in the pdb file (which, as expected, does not
> contain hydrogens).  Why is pdb2gmx looking for an atom that does
> not exist and should not?  Is there a naming convention in
> operation of which I am not aware?  Is pdb2gmx anticipating the
> naming of the hydrogens to be put in the structure? 
> >
> > If anyone has any insight into this problem, I would  be very
> grateful.  For the moment, it has stopped me in my tracks.
> >
> > Cheers,
> >
> > Seth
> >
> >
> >
> > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> >
> > Dr Seth Olsen, PhD
> > Postdoctoral Fellow, Computational Systems Biology Group
> > Centre for Computational Molecular Science
> > Chemistry Building,
> > The University of Queensland
> > Qld 4072, Brisbane, Australia
> >
> > tel (617) 33653732
> > fax (617) 33654623
> > email: s.olsen1 at uq.edu.au
> > Web: www.ccms.uq.edu.au
> >
> > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> >
> >
> >
> >
> > _______________________________________________
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,   75124 Uppsala, Sweden
> phone: 46 18 471 4205         fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au 

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