[gmx-users] N/A

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Mon Jan 22 14:37:37 CET 2007


On Friday 19 January 2007 15:25, sangeeta wrote:
> Dear Sir,
>      I have three questions,
>      My protein has +2 charge, so I added two Cl atoms through the program
> genion and subsequently edited the  topol.top file, in spite of that while
> running mdrun it gave an error that  "FATAL error, CL atom type can not be
> found",I can not understand the problem.

You have to add it to your .mdp file, too.

>      I wanted to include PBC in my simulation so in the pr.mdp file as well
> in md.mdp file I wrote PBC=xyz , am I correct? How can I know that PBC is
> being included in my simulation?
Yes, take a look at mdout.mdp

>       In spite of having dssp and running it I can not get the .xpm files.
> How can I generate those files?

do_dssp -h (set proper path to dssp binary)

>       Waiting for your reply.
> regards
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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
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 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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