[gmx-users] OPLS AA/M pdb2gmx error with inter

[Daniel Kozuch]

I am having a problem similar to that mentioned in a previous thread (
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg35369.html),
but I could not find a solution from that discussion. I am using pdb2gmx
with the flag -inter and the OPLS AA/M force field:

> gmx pdb2gmx -f ala.pdb -o ala.gro -inter
>> 23: OPLS-AA/M all-atom force field (2015 aminoacid dihedrals)
>>  7: None
>> 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
residue)
>>  1: ZWITTERION_COO- (only use with zwitterions containing exactly one
residue)

Fatal error:
tpA = 49549, i= 4 in print_atoms

The input structure is a pdb file from ALA from AmberTools (below) and I
have not modified the forcefield files. Was there any solution to this
error?

Best regards,
Dan

ATOM      1  N   ALA     1       3.326   1.548  -0.000  1.00  0.00
ATOM      2  H   ALA     1       3.909   0.724  -0.000  1.00  0.00
ATOM      3  CA  ALA     1       3.970   2.846  -0.000  1.00  0.00
ATOM      4  HA  ALA     1       3.672   3.400  -0.890  1.00  0.00
ATOM      5  CB  ALA     1       3.577   3.654   1.232  1.00  0.00
ATOM      6  HB1 ALA     1       3.877   3.116   2.131  1.00  0.00
ATOM      7  HB2 ALA     1       4.075   4.623   1.206  1.00  0.00
ATOM      8  HB3 ALA     1       2.497   3.801   1.241  1.00  0.00
ATOM      9  C   ALA     1       5.486   2.705  -0.000  1.00  0.00
ATOM     10  O   ALA     1       6.009   1.593  -0.000  1.00  0.00
TER
END