[gmx-users] Fw: problem with Justine tutorial

‪neda razavi‬ ‪ razavineda22 at yahoo.com
Sun Oct 4 19:41:40 CEST 2015

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  From: ‪neda razavi‬ ‪ <razavineda22 at yahoo.com>
 To: "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> 
 Sent: Sunday, 4 October 2015, 13:02:19
 Subject: problem with Justine tutorial

What does "add connectivity to our capping group" mean in KALP in DPPC Justine tutorial?
I am simulating KALP in DPPC through Justine tutorial and i faced this line. "we do not want pdb2gmx to build the normal amine and carboxyl groups. Instead, we want pdb2gmx to add connectivity to our capping groups"i want to khow what does "add connectivity" mean?Does it mean that we want pdb2gmx to take into account the bonds between kalp-15 and AC or NH2 capping groups?


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