[gmx-users] wrong format in input file ffamber03.hdb on line

[Justin A. Lemkul]

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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