[gmx-users] no residue type

[Nick Johans]

Hi, i,m a beginner. i us pdb2gmx or generating topology files.this is
aminoacid pdb file;

ATOM      1  N   HIS     1       0.102  -0.143   0.000  1.00  0.00
 N
ATOM      2  CA  HIS     1       1.558  -0.029   0.000  1.00  0.00
 C
ATOM      3  C   HIS     1       1.986   1.419   0.000  1.00  0.00
 C
ATOM      4  O   HIS     1       1.165   2.348   0.000  1.00  0.00
 O
ATOM      5  CB  HIS     1       2.047  -0.732  -1.277  1.00  0.00
 C
ATOM      6  CG  HIS     1       2.952  -1.892  -0.978  1.00  0.00
 C
ATOM      7  ND1 HIS     1       3.335  -2.320   0.291  1.00  0.00
 N
ATOM      8  CD2 HIS     1       3.517  -2.678  -1.972  1.00  0.00
 C
ATOM      9  CE1 HIS     1       4.118  -3.363  -0.046  1.00  0.00
 C
ATOM     10  NE2 HIS     1       4.282  -3.641  -1.368  1.00  0.00
 N
ATOM     11 1H   HIS     1      -0.540   0.725   0.000  1.00  0.00
 H
ATOM     12 2H   HIS     1      -0.397  -1.101   0.000  1.00  0.00
 H
ATOM     13  HA  HIS     1       1.928  -0.468   0.941  1.00  0.00
 H
ATOM     14 1HB  HIS     1       1.206  -1.113  -1.893  1.00  0.00
 H
ATOM     15 2HB  HIS     1       2.598  -0.031  -1.935  1.00  0.00
 H
ATOM     16  HD2 HIS     1       3.362  -2.530  -3.037  1.00  0.00
 H
ATOM     17  HE1 HIS     1       4.579  -3.923   0.758  1.00  0.00
 H
ATOM     18  HE2 HIS     1       4.837  -4.388  -1.810  1.00  0.00
 H
ATOM     19  OC  HIS     1       3.396   1.655   0.000  1.00  0.00
 O
ATOM     20  HC  HIS     1       3.896   0.754   0.000  1.00  0.00
 H
TER

i know i shouldn't  use AA as an independent structure so i try to add
termini by -ter then i choose amber99  and TIP3P water model but i get this
error;

In the chosen force field there is no residue type for 'HIS' as a starting
terminus

what should i do?
------------------------------
i used ambertools or generating .prmtop and .prcpd file. then
https://www.dropbox.com/s/rfjpz45we1f5h0z/amb2gmx_dihe_old.pl to convert
them to gromacs input file.

>> perl amb2gmx.pl --prmtop threonine.prmtop --crd threonine.inpcrd
--outname THRR


but thereis nothing in files as it says;
[roja at localhost cmd]$ perl amb2gmx.pl --prmtop threonine.prmtop --crd
threonine.inpcrd --outname THRR
sh: ambpdb: command not found
sh: rdparm: command not found
Parsing PDB file THRR.pdb...
found:
    0 protein or solute residues
    0 sodium ions
    0 chloride ions
    0 magnesium ions
    0 waters

    0 TOTAL residues read
Reading coordinates from CRD file...Reading prmtop file...
0 atom type indices read.

found:
        0 atoms
        0 bonds
        0 angles
        0 torsions
BAD BOX OR BOX NOT DETECTED; USING DUMMY BOX SIZE IN GRO FILEBAD BOX OR BOX
NOT DETECTED; USING DUMMY BOX SIZE IN GRO FILE
Qtot = 0
Qmax = 0 at atom -1

Constructing list of unique nonbonded atomtypes...
0 unique atomtypes found.
Writing atom types...
Done.
------------------------
is there sth i didn't consider?

Best regards
-Nick