[gmx-users] pdb2gmx problems and modified AA's
David
spoel at xray.bmc.uu.se
Sat Oct 9 12:05:46 CEST 2004
On Sat, 2004-10-09 at 11:29, Dr Seth Carlton OLSEN wrote:
> 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?
>
O2 is regarded as a C-terminal oxygen and is renamed to O. Your best bet
is renaming the O to something else.
As regards the HE31 etc. that should be possible to resolve by changing
atom names too.
> 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
>
> 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
>
>
>
>
> ----- 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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> >
>
> 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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