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

[Justin Lemkul]

On 9/23/19 12:39 PM, Daniel Kozuch wrote:
> 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?

There is a problem with the force field files. The terminal patching for 
a zwitterion requires oplsm_299 as the CA atom type, but no parameters 
for this atom are given in ffnonbonded_new.itp, nor is it listed in 
atomtypes.atp. I suggest contacting the authors to inquire about a 
solution/inclusion of the necessary parameters. The problem appears to 
be specific to zwitterion forms of amino acids.

-Justin

> 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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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