[gmx-users] obtaining a pdb after a simulation with ffamber

[Serena Leone]

Dear users,

I've been running a MD simulation on a protein using ffamber94 (from 
amber ports with gmx 3.3.1).

After the run, I extracted and minimized an average structure. I then 
converted the lowest energy structure (.gro) from the minimization in a 
pdb file with trjconv, but turns out some of the residues are 
misinterpreted, mostly cysteines. In particular, my initial structure 
pdb file, after re-editing for amberports, looked like this:

[...]
ATOM    960 2HB  SER A 201      68.231  51.739  23.034  1.00  0.00           H
ATOM    961  N   CYN A 202      67.790  48.850  25.290  1.00  0.00           N
ATOM    962  CA  CYN A 202      68.660  47.970  26.100  1.00  0.00           C
ATOM    963  C   CYN A 202      68.570  48.160  27.610  1.00  0.00           C
ATOM    964  O   CYN A 202      69.500  47.810  28.340  1.00  0.00           O
ATOM    965  CB  CYN A 202      70.100  48.040  25.590  1.00  0.00           C
ATOM    966  SG  CYN A 202      70.300  47.530  23.840  1.00  0.00           S
ATOM    967  H   CYN A 202      67.132  48.288  24.789  1.00 99.99           H
ATOM    968  HG  CYN A 202      71.615  47.722  23.789  1.00 99.99           H
ATOM    969  HA  CYN A 202      68.322  46.952  25.905  1.00  0.00           H
ATOM    970 1HB  CYN A 202      70.714  47.387  26.209  1.00  0.00           H
ATOM    971 2HB  CYN A 202      70.459  49.063  25.699  1.00  0.00           H
ATOM    972  N   ASN A 203      67.400  48.570  28.100  1.00  0.00           N
ATOM    973  CA  ASN A 203      67.150  48.800  29.530  1.00  0.00           C
[...]

The final structure, obtained with trjconv, for the same residue looks 
like this:

[...]
ATOM    953  HB2 SER A 201      72.090  52.980  29.520  1.00 99.99
ATOM    954  HG  SER A 201      71.240  53.080  27.400  1.00 99.99
ATOM    955  N   CYS A 202      70.360  50.550  31.680  1.00  0.00
ATOM    956  CA  CYS A 202      70.650  49.620  32.780  1.00  0.00
ATOM    957  C   CYS A 202      70.030  50.030  34.140  1.00  0.00
ATOM    958  O   CYS A 202      70.510  49.590  35.180  1.00  0.00
ATOM    959  CB  CYS A 202      72.170  49.350  32.860  1.00  0.00
ATOM    960  HB1 CYS A 202      72.360  48.630  33.660  1.00  0.00
ATOM    961  HB2 CYS A 202      72.710  50.270  33.080  1.00  0.00
ATOM    962  SG  CYS A 202      72.770  48.650  31.300  1.00  0.00
ATOM    963  HG  CYS A 202      72.430  49.690  30.540  1.00  0.00
ATOM    964  H   CYS A 202      69.810  50.170  30.930  1.00  0.00
ATOM    965  HA  CYS A 202      70.180  48.680  32.520  1.00  0.00
ATOM    966  H   CYS A 202      69.810  50.170  30.930  1.00 99.99
ATOM    967  HA  CYS A 202      70.180  48.680  32.520  1.00 99.99
ATOM    968  HB1 CYS A 202      72.360  48.630  33.660  1.00 99.99
ATOM    969  HB2 CYS A 202      72.710  50.270  33.080  1.00 99.99
ATOM    970  HG  CYS A 202      72.430  49.690  30.540  1.00 99.99
ATOM    971  N   ASN A 203      68.950  50.840  34.130  1.00  0.00
ATOM    972  CA  ASN A 203      68.160  51.190  35.300  1.00  0.00
[...]

meaning the residue is extended after the S atom of another methylene 
group (does the program think this is a S-S bond? CYS disulfide in 
ffamber are named CYS2...)

I also tried to manually edit the .gro file after the minimization 
changing the res names according to a "standard pdb" nomenclature, but 
it happens again... I wasn't able to find the cause of this behavior, 
and again, it's probably just something I'm overlooking. Does anybody 
have any suggestion?

Thanks a lot,

Serena






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