[gmx-users] Polyglycine PDB file.

[David van der Spoel]

On 2010-09-12 21.13, C Johnson wrote:
> I'm new to gmx so I'm just seeing if I'm able to make homoblock
> polypeptides. I would like to simulate a 5 residue polyglycine. I've
> used PRODRG to generate the pdb file, however trying to convert the file
> with pdb2gmx I receive the error:
>
> Fatal error:
> Residue 'Y' not found in residue topology database
>
> My pdb file is:
>
>
> ATOM 1 O GLY 1 -2.600 -2.350 -0.400 1.00 20.00 O
> ATOM 2 C GLY 1 -2.250 -1.400 0.340 1.00 20.00 C
> ATOM 3 O GLY 1 -1.850 -1.490 1.520 1.00 20.00 O
> ATOM 4 CA GLY 1 -2.330 0.010 -0.240 1.00 20.00 C
> ATOM 5 N GLY 1 -3.620 0.630 0.130 1.00 20.00 N
> ATOM 6 C GLY 2 -3.800 1.640 1.000 1.00 20.00 C
> ATOM 7 O GLY 2 -4.910 2.110 1.230 1.00 20.00 O
> ATOM 8 CA GLY 2 -2.600 2.240 1.730 1.00 20.00 C
> ATOM 9 N GLY 2 -2.160 3.460 1.030 1.00 20.00 N
> ATOM 10 C GLY 3 -2.510 4.720 1.320 1.00 20.00 C
> ATOM 11 O GLY 3 -2.050 5.670 0.680 1.00 20.00 O
> ATOM 12 CA GLY 3 -3.510 4.990 2.460 1.00 20.00 C
> ATOM 13 N GLY 3 -4.640 5.790 1.950 1.00 20.00 N
> ATOM 14 C GLY 4 -5.930 5.680 2.300 1.00 20.00 C
> ATOM 15 O GLY 4 -6.800 6.390 1.810 1.00 20.00 O
> ATOM 16 CA GLY 4 -6.340 4.640 3.360 1.00 20.00 C
> ATOM 17 N GLY 4 -6.800 5.360 4.570 1.00 20.00 N
> ATOM 18 C GLY 5 -7.330 4.810 5.670 1.00 20.00 C
> ATOM 19 O GLY 5 -7.640 5.500 6.640 1.00 20.00 O
> ATOM 20 CA GLY 5 -7.550 3.300 5.730 1.00 20.00 C
> ATOM 21 N GLY 5 -8.990 3.000 5.660 1.00 20.00 N
> END
>
> I'm not sure what I could be doing wrong since I pretty much mimicked
> the speptide.pdb in the tutor file.
>
> Thanks for the help,
> Joe.
>
I guess your pdb file has been damaged by a text editor (Word?). PDB 
files are fixed format, you can not add or remove spaces at will. You 
could try clicking together a peptide in Pymol or so, or drop the prodrg 
output in Notepad (if you're on Windows). On mac or linux it should be 
straightforward with text editors.



-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se