[gmx-users] Capping groups

[Justin Lemkul]

On 5/6/14, 5:18 AM, Balasubramanian Suriyanarayanan wrote:
> Dear all
> In membrane protein simulation do we need to treat the Protein with lipid
> model with Leap module of AMBER before pdb2gmx step. what is the point in

No idea what this means.

> giving "none" option  in response to -ter command. where we have capped N
> and C termini before pdb2gmx command? Please clarify.
>

Normal termini in Gromacs are built based on the assumption that a polypeptide 
chain has free amine and carboxyl groups at the respective termini, so pdb2gmx 
acts accordingly to build whatever H and O atoms are needed.  In the case of 
capping groups, no such manipulation should be applied, hence you choose "None" 
to signify that no changes should be made to the atoms present.

-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 601
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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