[gmx-users] Problem building a new polymer using pdb2gmx....

[David van der Spoel]

Alberto Sergio Garay wrote:
> Dear users
> 
> I'm trying to build a polymer with a new building block. I have included 
> the new
> topology block inside the force field rtp file, which I've choosen for 
> my simulation (ffG53a6.rtp).
> I've also prepared a gro input file, where the atoms of each residue 
> follows the same order as in the rtp file
> I also added the new residues names in aminoacids.dat
> 
> The problem is: when I run pdb2gmx to obtain the topology of my system 
> it gives me the following error:
> 
> Fatal error:
> Atom H1 in residue VBT 2 not found in rtp entry with 24 atoms
>              while sorting atoms. Maybe different protonation state.
>              Remove this hydrogen or choose a different protonation state.
>              Option -ignh will ignore all hydrogens in the input.
> 
> But there's no H1 atom in my residues. Is pdb2gmx including some extra 
> atoms to complete my molecule?
> Could anyone give any clue about my problem?

yes. pdb2gmx thinks your molecule is a protein and want to add Hydrogens 
to the termini. Use the -ter flag and select None.
> 
> Tank you in advance.
> 
> Sergio
> 
> below there's a part of my rtp file
> ...
> [ VBT ]
>  [ atoms ]
> ; name   type   charge   chargegroup
>   CC1   CH2     0.00000     1
>   CC2   CH1     0.12000     2
>   CR1     C    -0.12000     3
>   CR2     C    -0.14000     4
>   HR2    HC     0.14000     4
>   CR3     C    -0.08000     5
>   HR3    HC     0.08000     5
>   CR4     C    -0.05000     6
>   CT1   CH2     0.37000     6
>   NT1    NR    -0.32000     6
>   CR5     C    -0.13000     7
>   HR5    HC     0.13000     7
>   CR6     C    -0.17000     8
>   HR6    HC     0.17000     8
>   CT2     C    -0.21000     9
>   HT1    HC     0.21000     9
>   CT3     C    -0.09000    10
>   CT4   CH3     0.09000    10
>   CT5     C     0.58000    11
>   OT1     O    -0.58000    11
>   NT2    NR    -0.22000    12
>   HT2     H     0.22000    12
>   CT6     C     0.54000    13
>   OT2     O    -0.54000    13
> 
> part of my *.gro file
> 
>     2VBT    CC1   21   3.221   5.305   1.589
>     2VBT    CC2   22   3.143   5.334   1.460
>     2VBT    CR1   23   3.115   5.221   1.384
>     2VBT    CR2   24   3.196   5.155   1.293
>     2VBT    HR2   25   3.305   5.159   1.298
>     2VBT    CR3   26   3.132   5.074   1.200
>     2VBT    HR3   27   3.198   5.003   1.151
>     2VBT    CR4   28   2.995   5.068   1.175
>     2VBT    CT1   29   2.948   5.023   1.052
>     2VBT    NT1   30   3.028   5.038   0.928
>     2VBT    CR5   31   2.919   5.144   1.263
>     2VBT    HR5   32   2.810   5.142   1.268
>     2VBT    CR6   33   2.977   5.208   1.372
>     2VBT    HR6   34   2.916   5.232   1.459
>     2VBT    CT2   35   3.070   4.916   0.874
>     2VBT    HT1   36   3.009   4.827   0.860
>     2VBT    CT3   37   3.190   4.911   0.804
>     2VBT    CT4   38   3.245   4.779   0.750
>     2VBT    CT5   39   3.264   5.027   0.784
>     2VBT    OT1   40   3.364   5.030   0.712
>     2VBT    NT2   41   3.224   5.150   0.839
>     2VBT    HT2   42   3.293   5.223   0.844
>     2VBT    CT6   43   3.100   5.156   0.903
>     2VBT    OT2   44   3.076   5.266   0.952
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se