[gmx-users] N/A

[sangeeta]

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.
    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?
     In spite of having dssp and running it I can not get the .xpm files. 
Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx
are being produced.How can I generate those files?  
     Waiting for your reply.

regards
SANGEETA 

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