Converting pdb file with pdb2towhee

Dear everyone,

I have a problem with pdb2towhee utility program. Indeed, I generate a .pdb
file with Web Lab and tried to convert it with pdb2towhee to generate a
towhee_coords and towhee_altinp input files. But it results the following
error message :

« At line 323 of file pdb2towhee.F (unit=20, file=’graphene_final3.pdb’)

Fortran runtime error : Expected INTEGER for item 6 in formatted transfer, got
CHARACTER

(A6, I5, 1x, A4, 1x, A3, 2x, i4, 4x, 3f8.3) » with the sign ̂̂below i4.

To the questions, I answer :

First : Type of input file : 2-generic pdb file

Second : pdb filename : ’graphene_final3.pdb

Third : Number of atoms : 34

Fourth : Shift atom positions : FALSE

With TRUE at the last question, it results the same error message.

I tried with two different .pdb files :

First:

ATOM 1 C -4.256 1.792 -0.023

ATOM 2 C -4.266 0.395 -0.201

Second:

ATOM 1 C 0 -4.256 1.792 -0.023

ATOM 2 C 0 -4.266 0.395 -0.201

Lastly, I also started with some of provided examples , like « UFF ». This
example generates .pdb files. So, I tried to convert one of them with
pdb2towhee. And I have the same error than before.

Thank you very much,

Nicolas

Yep, looks like there is a formatting error in that bit of code as we are
really using a character string for what should be an integer, I think that
was to avoid an error in the cases where no aminonumber is provided, but then
the wrong formatting made it into the code.

I have fixed this and will be releasing it in version 6.2.9.

Thanks for your bug report.

Marcus

Thank you for answering.

Further more, I tried to use xyz2towhee. But it doesn't convert the xyz file I
had generated with WebLab.

The xyz file I generated is below:

34

GRAPHENE 0.000000

C -4.2560 1.7920 -0.0230

C -4.2660 0.3950 -0.2010

C -3.0620 2.4720 0.1420

C -3.0730 -0.3230 -0.2200

C -1.8300 1.7690 0.1300

C 4.2640 -0.4020 0.0910

C -1.8400 0.3700 -0.0570

C 3.0610 -2.4770 -0.2670

C 3.0690 0.3080 0.1620

C -0.5820 2.4480 0.2990

C -0.6080 -0.3520 -0.0900

C -3.0610 -1.7660 -0.4040

C 0.6030 0.3330 0.0650

C 0.6110 1.7540 0.2690

C -0.6160 -1.7730 -0.2910

C 1.8360 -0.3860 0.0100

C 1.8870 2.4340 0.4380

C 0.5780 -2.4650 -0.3430

C -1.8930 -2.4560 -0.4390

C 1.8270 -1.7820 -0.1990

C 3.0560 1.7460 0.3870

C 4.2570 -1.7930 -0.1280

H -3.0770 3.5660 0.2790

H -4.0130 -2.3110 -0.5210

H -1.9190 -3.5490 -0.5840

H 1.9110 3.5230 0.6080

H -5.2300 -0.1230 -0.3300

H -5.2080 2.3480 -0.0160

H 0.5720 -3.5560 -0.5020

H -0.5760 3.5400 0.4510

H 3.0780 -3.5660 -0.4350

H 5.2110 -2.3410 -0.1870

H 5.2290 0.1190 0.2030

H 4.0070 2.2890 0.5160

Could you tell me what's wrong with this file?

Or if you have an example of xyz file which can be converted into pdb file
with xyz2towhee, I am interested in seeing it.

Thank you very much,

Nicolas

I need not mean a particular xyz format in the naming of this file, this is
just a generic conversion routine of 3 coordinate system into a format useful
for starting position input files.

This is the sort of program I end up using and modifying to convert from
whatever general xyz format I have into something else that I need. If you
look inside at the program you will see the information it requires, but it is
intended as an example for you to freely modify for your particular xyz
format.

Marcus