[gmx-users] pdb2gmx + rmsd from native structure

[Rainer Böckmann]

On Sat, 26 Feb 2005, Ivica Res wrote:

> Dear Users,
>
> I am trying to relax a protein from its natural state. The problem is
> that initial *.gro file is already 3A rmsd away from the native protein.
> I used
> pdb2gmx -f 1MCT.pdb -o 1mct.gro -p 1mct.top
> (where  1MCT.pdb is one of the 2 chains from initial structure, and I
> removed the hydrogens)
>
> Now
> g_confrms -f1 1MCT.pdb -f2 1mct.gro
> (using  option 2 (   Protein-H)) gives rms 0.3nm).
>
> The main difference between 1MCT.pdb and 1mct.gro should be that
> 1mct.gro has hydrogens.
> Can anybody explain what is the reason for this rmsa of 3A , and how can
> it be avoided (I would like to start as close to initial structure as
> posible).
>
> Thanks,
> Ivica
>
> PS:
> g_confrms gives me the warning that "1145 atomnames did not match". Visual
> inspection shows that some atoms in 1mct.gro are rearanged compared to
> 1MCT.pdb (for example, order N, CA, C, O, CB in native structure 1MCT.pdb
> becomes N, CA, CB, C, O in 1mct.gro, resulting in the warning
> atomnames at index 3 don't match: 3 C, 6 CB). Is this related to above
> problem?

yes - in order to compare the two pdb-files with different number of atoms
you have to supply index-files. chose index-groups with the same atoms...
cheers, rainer

> Here is the first residue in both files:
>
>                       1mct.gro:
>      1ILE      N    1  -1.240   1.924   0.885
>      1ILE     H1    2  -1.236   2.024   0.882
>      1ILE     H2    3  -1.148   1.887   0.869
>      1ILE     H3    4  -1.302   1.891   0.814
>      1ILE     CA    5  -1.288   1.881   1.019
>      1ILE     HA    6  -1.224   1.916   1.087
>      1ILE     CB    7  -1.433   1.936   1.047
>      1ILE     HB    8  -1.497   1.905   0.976
>      1ILE    CG1    9  -1.434   2.091   1.045
>      1ILE   HG11   10  -1.387   2.121   0.963
>      1ILE   HG12   11  -1.529   2.122   1.042
>      1ILE    CG2   12  -1.483   1.882   1.182
>      1ILE   HG21   13  -1.575   1.916   1.200
>      1ILE   HG22   14  -1.485   1.782   1.179
>      1ILE   HG23   15  -1.421   1.912   1.255
>      1ILE     CD   16  -1.368   2.158   1.163
>      1ILE    HD1   17  -1.374   2.257   1.152
>      1ILE    HD2   18  -1.415   2.131   1.247
>      1ILE    HD3   19  -1.272   2.131   1.167
>      1ILE      C   20  -1.292   1.727   1.018
>      1ILE      O   21  -1.361   1.669   0.934
>
>                   1MCT.pdb:
> ATOM      1  N   ILE A  16     -12.396  19.242   8.850  1.00  8.19
> ATOM      2  CA  ILE A  16     -12.881  18.808  10.189  1.00  9.20
> ATOM      3  C   ILE A  16     -12.916  17.275  10.179  1.00 10.50
> ATOM      4  O   ILE A  16     -13.607  16.689   9.344  1.00  9.60
> ATOM      5  CB  ILE A  16     -14.332  19.358  10.468  1.00  9.72
> ATOM      6  CG1 ILE A  16     -14.341  20.905  10.450  1.00  8.90
> ATOM      7  CG2 ILE A  16     -14.828  18.817  11.820  1.00 11.81
> ATOM      8  CD1 ILE A  16     -13.682  21.580  11.625  1.00 14.04
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