drugdesign wrote:
Dear Gromacs users,
I am getting and eeror while loading Amber03 force field by pdb2gmx command:
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.2
Source code file: h_db.c, line: 87
Fatal error:
wrong format in input file ffamber03.hdb on line
2 7 OW
-------------------------------------------------------
Because it is improperly formatted. See the manual for proper formatting.
Where did you get that .hdb file? The ones disributed with the ffamber ports
have always worked for me:
http://chemistry.csulb.edu/ffamber/
Where can I get spc.itp and spc216.gro
There are in the share/top subdirectory of your Gromacs installation.
In tutorial it is reffered to mdcourse directory, bu I do not have such a
directory.
Probably because you were supposed to download some files from wherever you've
found the tutorial.
I also wonder where I can get TIP3P.gro and .itp files and also the same TIP4P
files.
Since both SPC and TIP3P are 3-point water models, you can use spc216.gro and
apply the tip3p.itp parameters (tip3p.itp is also in share/top). Then equilibrate.
TIP4P files (.gro and .itp) are also in share/top.
-Justin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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