Hi Chris,
I am not sure if this is a typo in your input file or just the email but
the last two lines should read:
END
END
and not "RND"
Also, the final / - place it in column 2 just to be sure. I.e. with just a
single space before it.
All the best
Ross
On 9/10/12 5:31 PM, "Chris Chris" <alpharecept.yahoo.com> wrote:
>I am using Amber 11 on Blacklight (PSC). I am trying to equilibrate my
>protein as is done in the MMPBSA tutorial online. I am using pmemd.
>
>Here is my .in file:
>
>heat 2psj ctz first time
>
> &cntrl
>
> imin=0,irest=1,ntx=5,
>
> nstlim=25000,dt=0.002,
>
> ntc=2,ntf=2,
>
> cut=8.0, ntb=2, ntp=1, taup=1.0,
>
> ntpr=500, ntwx=500,
>
> ntt=3, gamma_ln=2.0,
>
> temp0=300.0,
>
> ntr=1,
>
> /
>
>lets' just write this
>
>10.0
>
>RES 1 612
>
>RND
>
>END
>
>
>
>My equilibration stops when it reaches this point and I am assuming that
>my .in file is written incorrectly for pmemd.
>
>Can someone correct me?
>
>Thanks
>
>Chris
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Received on Mon Sep 10 2012 - 16:00:06 PDT
