[gmx-users] Re: problem with pdb2gmx and ffG43a1p

[Xavier Periole]

Hi,

concerning the personal email. It is fine but you always have more chances
to get an answer from the user list than from one individue. Furthermore
it is important to keep a record of all the conversations, this might
help some one some day. Thus I suggest we converse on the user-list.

Did you modify the ffG43a1p.hdb file?

It does not make too much sense to me as pdb2gmx reports and
error on the water molecule, which should not have been modified.
You should get the manual the building of hydrogens is described
somewhere. Check which part is wrong in the file you use.

XAvier
> Hi
> I am really sorry but I had to write a personal mail as I am quite new to
> this field.
> I started everything from scratch again.
> 
> I am using ffG43a1p & Gromacs 3.3.1-4 for a simulating a phosphorylated
> protein.
> I have added the phosphate, which is represented  like this in my PDB file:
> ATOM      8  N   SEP A  17      17.566 -23.560  -6.457  0.00  0.00
> N
> ATOM      9  CA  SEP A  17      17.870 -24.758  -7.222  0.00  0.00
> C
> ATOM     10  C   SEP A  17      16.890 -25.866  -6.744  0.00  0.00
> C
> ATOM     11  O   SEP A  17      16.495 -25.823  -5.572  0.00  0.00
> O
> ATOM     12  CB  SEP A  17      19.334 -25.174  -7.057  0.00  0.00
> C
> ATOM     13  OG  SEP A  17      19.653 -26.353  -7.804   0.00  0.00
> O
> ATOM     14  P   SEP A  17      21.178 -26.666  -7.707  0.00  0.00
> P
> ATOM     15  O1P SEP A  17      21.803 -26.649  -9.136  0.00  0.00
> O
> ATOM     16  O2P SEP A  17      21.380 -28.074  -7.067  0.00  0.00
> O
> ATOM     17  O3P SEP A  17      21.876 -25.589  -6.822  0.00  0.00
> O
> 
> But whenever I try pdb2gmx, it throws me an this error:
> Program pdb2gmx, VERSION 3.3.1
> Source code file: h_db.c, line: 85
> 
>Fatal error:
> wrong format in input file ffG43a1p.hdb on line
>        2       7       OW
> 
> 
> Is this error  because I am using a newer version of GROMACS or there is
> something wrong with my PDB  file (SEP) representation.
> Unphosphorylated protein gives  no problem with  other FF, but same error is
> thrown with  ffG43a1p.
> 
> Best,
> -- 
> Ambrish Roy
> 
> Graduate Student
> Bioinformatics Center
> University of Kansas
> 2030 Becker Dr
> Lawrence, KS 66047

-----------------------------------------------------
XAvier Periole - PhD

1- Institute of Molecular Assemblies
      City University of New York - USA
2- Molecular Dynamics-Group
      University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
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