[gmx-users] Errors during energy minimization of POPC membrane

[Justin Lemkul]

On 10/8/16 1:10 PM, Roshan Shrestha wrote:
> Justin,
>          I have attached here with both my POPC membrane that I have created
> using charmm gui builder and the topology file. Still in dilemma, what caused so
> many errors during its energy minimization.
>

The topology defines angles for the water molecules, which it should not. 
Remove the waters from the [atoms] and all bonded directives.  The #include 
statement for TIP3P takes care of all the waters.

-Justin

> --
> Roshan Shrestha
> Graduate Student
> Central Department of Physics,Tribhuvan University
> Kathmandu,Nepal
>
>

-- 
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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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