[gmx-users] pdb2gmx: S-S bond

David spoel at xray.bmc.uu.se
Sun Jul 7 20:09:02 CEST 2002

On Sun, 2002-07-07 at 18:42, Mateusz Nowak wrote:
> Hi!
> I have produced topology file for protein with pdb2gmx v. 3.0, using
> Gromos96 43a1 forcefield. There are some disulfide bonds there, but when I
> look at top file, there are not bond type codes assigned to S-S atom pairs
> in [ bonds ], although the pairs themselves are specified there. Is this
> ok, if [ bonds ] for S-S remains empty?
> I can see in ffG43a1bon.itp file that this bond should be of gb_33 type.
> Should I fill this manually in top file?
If you run grompp it will tell you when information is missing. As a
rule you should not get line like:
no bonded parameters for a -b, line XXX topol.top, using zeroes.
(unless you know what you are doing is correct of course).

In general if you get zero warnings your input is OK.
You can check the resulting topology with gmxcheck.
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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