AMBER Archive (2007)

Subject: Re: AMBER: restraint in minimization

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Mar 22 2007 - 05:14:22 CST

try restraintmask='7-20,26-38'
for more information, please read the manual, there is
an example of just this kind of selection. p287 for amber9.

On 3/22/07, deepti nayar <deepti.icgeb_at_gmail.com> wrote:
> hi amber users
>
> I am using restraint command in sander during minimization of a
> dipeptide (phenylalanine- dehydrophenylalanine). I a using the
> following command which is giving thew following error
>
>
>
> [root_at_Bic11 exe]# sander -O -i min.in -o delphe_rest.min.out -c
> delphe_rest.x -p prmtop -r delphe_rest.min.x
>
> At line 1022 of file _mdread.f (Unit 5 "min.in")
> Traceback: not available, compile with -ftrace=frame or -ftrace=full
> Fortran runtime error: In line 1 of namelist cntrl:
> Bad name
> restraintmask=':7-20', '
>
> ^
>
> I have to restrain the movement of atoms 7-20 and 26-38
>
>
> i am giving the following input file
>
>
> min.in
>
> energy minimization for delphe starting structure
>
> &cntrl
> imin=1, maxcyc=10, ncyc=5, ntpr=1,
> ntb=0,cut=15.0, ntr=1, restraint_wt=1.0,
> restraintmask=':7-20', ':26-38',
> &end
> &ewald
> eedmeth=5,
> &end
>
>
> i cant understand where i am going wrong
>
> please guide me
>
> thanks
> deepti
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