[gmx-users] pdb2gmx + rmsd from native structure

[Ivica Res]

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?
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