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

[David]

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 the
hydrogens 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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