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
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