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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