[gmx-users] Fw: problem with Justine tutorial

[Justin Lemkul]

On 10/4/15 1:27 PM, ‪neda razavi‬ ‪ wrote:
>
>      ----- Forwarded Message -----
>    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?
>

"Add connectivity to the capping groups" means precisely what it says.  You 
don't have free NH3+ or COO- termini; you have acetyl and amide groups.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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