GROMACS version: 2019.4
GROMACS modification: No
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Hello. I am trying out protein-ligand molecular dynamics, following the tutorial by Justin A. Lemkul, with modifications to suit mostly my ligand. I am using the gromos54a7_atb.ff, since my ligand could only be processed using ATB. I am however encountering an error (in fact 25 errors but all similar and emanating from the ligand, I guess) when I get to the step of adding ions, the error reads:
ERROR 1 [file topol.top, line 21783]:
atom Br3 (Res 5b-1) has mass 0 (state A) / 0 (state B)
The other 24 errors say the same thing but different atoms. I am failing to figure out how to solve this problem. Please assist.
Hi,
did you check if the atom masses are properly defined in force fields file both for state A and B? Mass are defined under the directive [ atomtypes ] and [atoms] in the force field and topology files and in atomtypes.atp.
\Alessandra
Hello
Yes, I have checked the [atomtypes.atp] and it looks fine. In the topology files, I am not quite sure. The [topol.top] does not include the ligand in the [atoms] section for both state A and B, but in my [ligand.itp] the masses are defined well. Though there is no classification of State A and B in the [ligand.itp]. Is there any other file I need to check?
Hi,
Sorry I did not understand: Did you check also gromos54a7_atb.ff/ffnonbonded.itp?
Alessandra
Hello
Sorry I had not checked the gromos54a7_atb.ff/ffnonbonded.itp, yes it seems that’s where the problem is. All the masses have a value of 0, how can I rectify this?
Hi
To check if the problem is really there, you can just correct the mass of Br3 atom and see if the first error disappear.
\Alessandra
Hello
Yes, the problem was with the gromos54a7_atb.ff/ffnonbonded.itp, and correcting the masses solved the problem. Thank you very much for your assistance, greatly appreciate it.