AMBER Archive (2007)

Subject: Re: AMBER: umbrella sampling

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Nov 25 2007 - 13:52:57 CST

I suggest first trying to set up and have it run with just
2 atoms, not CM restraints. when that works, switch to the
CM definition.
I'm not sure if you're including that &rst definition in the mdin file
or if that is from d1.rest. it probably should be in the d1.rst file.
it's also not clear where the file name "d1.restraint" in the error comes
from,
since you don't have that actual name anywhere in the inputs that
you sent us.

also let us know what amber version you are using, or else it
is very hard to say what's going on since these things do change
with different versions.

On Nov 25, 2007 2:32 PM, Jardas sucuriba <jarda_s_at_hotmail.com> wrote:

>
> Hi,
>
> When I try to run my input files for umbrella sampling I obtain the
> following error:
>
>
>
> PGFIO-F-239/namelist read/unit=33/entity name is not member of group.
>
> File name = d1.restraint formatted, sequential access record = 5
>
> In source file _restal.f, at line number 311
>
> p1_27940: p4_error: net_recv read: probable EOF on socket: 1
>
> rm_l_1_27941: (1.203240) net_send: could not write to fd=5, errno = 32
>
>
>
> I didn´t manage to find where is the error. Does anyone know what I am
> doing wrong?
>
> Here is my input file:
>
>
>
> md
>
> &cntrl
>
> imin = 0, irest=1, ntx=5,
>
> nstlim=25000, dt=0.002, scee = 1.2,
>
> ntt=3, gamma_ln=1.0, tempi=300.0, temp0=300.0,
>
> ntb = 2, ntp=1, pres0=1.0,
>
> taup=2.0,
>
> ntc=2, ntf=2,
>
> ntr = 0,
>
> nmropt=1,
>
> ntwe=100, ntwx=100, ntpr=100,
>
> cut = 10.0
>
> /
>
> &wt type='DUMPFREQ', istep1=1 /
>
> &wt type='END' /
>
> DISANG=d1.rest
>
> DUMPAVE=d1.res
>
>
>
> #distance restrainst
>
> &rst iat=-1,-1, r1=0.0, r2=4.575, r3=4.575, r4=100.0, rk2=10., rk3=10.,
>
> iresid=1,
>
> IGR1=262, IGR2=267,267,267,
>
> GRNAM1(1)=SG,
>
> GRNAM2(1)=C19, GRNAM2(2)=C20, GRNAM2(3)=O1,
>
> /
>
>
>
> The idea is to approach the SG atom of a cysteine to the center of mass of
> 3 atoms of a ligand.
>
>
>
> Thanks
>
> Jardas
>
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>

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