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

[Mark Abraham]

Serena Leone wrote:
> 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...)

There's no added methylene... all five H atoms from CYS have been 
duplicated and are now coincident. You should look at the output 
structure file from pdb2gmx and you will probably see that the 
duplication occurred there. Perhaps the name CYN confused things. If so, 
you should re-do pdb2gmx and read carefully the messages it outputs, and 
potentially change your selections suitably.

> 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?

I don't follow what you think you're trying to achieve here. 
Copied-and-pasted command lines always enhance descriptions of 
operations. That way we don't have to deal with any (erroneous) 
filtering that might be going on inside your head :-)

Mark