I am trying to use the following command in GROMACS to generate a CHARMM topology file:
gmx pdb2gmx -ff charmm27 -f amp.pdb -o amp.gro -p amp.top
The atom list in my pdb file (amp.pdb) is:
ATOM 1 N6 RA A 1 0.498 2.821 0.753 1.00 0.00 N
ATOM 2 C6 RA A 1 -0.060 1.526 0.656 1.00 0.00 C
ATOM 3 H61 RA A 1 1.489 2.989 0.529 1.00 0.00 H
ATOM 4 H62 RA A 1 -0.087 3.615 1.052 1.00 0.00 H
ATOM 5 N1 RA A 1 -1.376 1.310 0.955 1.00 0.00 N
ATOM 6 C5 RA A 1 0.696 0.429 0.257 1.00 0.00 C
ATOM 7 C2 RA A 1 -1.934 0.060 0.867 1.00 0.00 C
ATOM 8 C4 RA A 1 0.124 -0.797 0.176 1.00 0.00 C
ATOM 9 N3 RA A 1 -1.181 -1.011 0.473 1.00 0.00 N
ATOM 10 H2 RA A 1 -2.979 -0.080 1.110 1.00 0.00 H
ATOM 11 N7 RA A 1 1.994 0.358 -0.092 1.00 0.00 N
ATOM 12 N9 RA A 1 1.043 -1.691 -0.226 1.00 0.00 N
ATOM 13 C8 RA A 1 2.175 -0.957 -0.383 1.00 0.00 C
ATOM 14 H8 RA A 1 3.122 -1.368 -0.708 1.00 0.00 H
ATOM 15 C4' RA A 1 -0.345 -4.785 0.483 1.00 0.00 C
ATOM 16 C3' RA A 1 1.095 -5.264 0.345 1.00 0.00 C
ATOM 17 C2' RA A 1 1.782 -3.941 0.483 1.00 0.00 C
ATOM 18 C1' RA A 1 0.894 -3.132 -0.459 1.00 0.00 C
ATOM 19 O4' RA A 1 -0.440 -3.570 -0.241 1.00 0.00 O
ATOM 20 O2' RA A 1 3.122 -3.963 0.073 1.00 0.00 O
ATOM 21 H2'1 RA A 1 3.620 -4.457 0.776 1.00 0.00 H
ATOM 22 H2'2 RA A 1 1.677 -3.545 1.523 1.00 0.00 H
ATOM 23 O3' RA A 1 1.463 -6.177 1.336 1.00 0.00 O
ATOM 24 H3' RA A 1 1.281 -5.686 -0.671 1.00 0.00 H
ATOM 25 C5' RA A 1 -1.349 -5.820 -0.028 1.00 0.00 C
ATOM 26 H4' RA A 1 -0.561 -4.555 1.553 1.00 0.00 H
ATOM 27 O5' RA A 1 -2.649 -5.309 0.126 1.00 0.00 O
ATOM 28 H5'1 RA A 1 -1.225 -6.749 0.574 1.00 0.00 H
ATOM 29 H5'2 RA A 1 -1.133 -6.018 -1.103 1.00 0.00 H
ATOM 30 P RA A 1 -3.753 -6.519 -0.472 1.00 0.00 P
ATOM 31 O1P RA A 1 -4.757 -5.364 -1.290 1.00 0.00 O
ATOM 32 O2P RA A 1 -4.714 -6.522 0.973 1.00 0.00 O
ATOM 33 H1' RA A 1 1.146 -3.365 -1.520 1.00 0.00 H
I get the warning:
WARNING: there were 3 atoms with zero occupancy and 28 atoms with
occupancy unequal to one (out of 33 atoms). Check your pdb file.
And a fatal error:
Fatal error:
atom N not found in buiding block 1RA while combining tdb and rtp
Does anyone have a working AMP pdb file, or know what is wrong with my atom list above?
Hi Iskinder! You shall check rtp-residue for you molecule in the force field folder which is placed in the folder inside gromacs with the name top (there are all forde field folders in there). Your structure has to match the residue with the name RA.
Hi Iskinder,
Please verify the topology file for the errrors.
You may try to simulate the pdb using OPLS-AA/L all-atom force field and verify the top files.
Thanks,
Rajesh
Thank you very much Inna Ermilova and Rajesh Durairaj
Unfortunately, nothing worked so far. The PDB file is attached. If you could give it a look that will be highly appreciated.
The command I am using is:
gmx pdb2gmx -ff charmm27 -f amp.pdb -o amp.gro -p amp.top
I still get the error message:
Fatal error:
atom N not found in buiding block 1RA while combining tdb and rtp
Hi Iskinder! You shall draw your structure according to rtp-residue, i.e. in the same order as there, naming atoms like there, then it will work.
Reordering my atoms doesn't seem to fix the error. The rtp-residue from the CHARMM directory, and my structure are both attached here. I have made them identical, yet the error persists. Any idea? Inna Ermilova
Iskinder, if you have a total match with names with rtp-residue, but get the same error then it can be one of 2 reasons:
1. You run the old file
2. When you changed the names you shifted them so gromacs is not reading them like N7, but reads only N (the first part).
I would suggest you not to mix coordinates but try to draw the structure following the order in rtp-residue. Then rename atoms according to it without shifting atomic names and coordinates (keep the same spaces as they should be). Then it has to work. The error which you get is well known. There can not be too many variations.
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