AMBER Archive (2008)

Subject: Re: AMBER: distance restraint in minimization

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Dec 17 2008 - 12:15:24 CST

Hi,

I just recompiled amber and it seems to be working well, i changed the
maxatoms from 5,000 to 50,000 now when i create the RST.f file i get this

[Taufik_at_sb2051B-9 CEBP8]$ makeDIST_RST -upb fixbond -pdb CEBP8.pdb -rst
RST2.f
# makeDIST_RST
Currently configured for up to 50000 atoms
Using MAP file /usr/local/Programs/amber10.09/dat/map.DG-AMBER

The number of atoms has changed. The output (RST.f and RST2.f) are
exactly the same, before and after modifying global.h

yet when i try
>sander -O -i minimize.in -o CEBP8.out -c CEBP8.inpcrd -p CEBP8.prmtop
-r CEBP8.rst
i get >At line 841 of file _nmrcal.f
Fortran runtime error: End of file

not sure what is wrong, my minimize.in file is
CEBP8 minimization of 20,000 steps
&cntrl
  imin = 1,
  maxcyc = 20000,
  ncyc = 10000,
  ntb = 1,
  ntr = 0,
  cut = 10,
  nmropt = 1,
/
&wt type='REST’, istep1=0,istep2=5000,value1=0.1,value2=4.0, /
&wt type=’REST’, istep1=5001,istep2=20000,value1=4.0,value2=4.0, /

&wt type=’END’ /
DISANG = RST2.f

Thank you for your help,
Taufik

luzhenw1_at_msu.edu wrote:
> First, you need change the global.h
> file,(/opt/amber9/src/nmr_aux/prepare_input/global.h), change the
> maxatoms to whatever number you want. probably you need re-compile amber.
>
> Second, copy the /usr/local/Programs/amber10.09/dat/map.DG-AMBER
> to some place you can modify it, add your own atom type at the end
> following the its own format.
>
> hope this will help.
>
> zhenwei
>
> 引用 "Taufik Al-Sarraj" <taufik.alsarraj_at_utoronto.ca>：
>
> > Thank you David,
> > I changed the input file to this
> > CEBP minimization of 20,000 steps
> > &cntrl
> > imin = 1,
> > maxcyc = 20000,
> > ncyc = 10000,
> > ntb = 1,
> > ntr = 0,
> > cut = 10,
> > nmropt = 1,
> > /
> > DISANG = RST.f
> >
> >
> > i read the help file and i need to use makeDIST_RST function
> > so i created a fixbond file
> > "11 ASN ND2 142 T O4 2.5
> > 11 ASN ND2 143 T O4 5.5
> > 69 ASN ND2 121 T O4 2.5
> > 69 ASN ND2 122 T O4 5.5"
> >
> > and i used > makeDIST_RST -upb fixbond -pdb *.pdb -rst RST.f
> > i got an error > # makeDIST_RST
> > Currently configured for up to 5000 atoms
> > Using MAP file /usr/local/Programs/amber10.09/dat/map.DG-AMBER
> > ERROR no map function for O4 T :data= 11 ASN ND2 142 T O4 2.5
> >
> > this means i should modify map.DG-AMBER or should i add D in front of
> > the T in my fixbond file and also in my pdb file?
> >
> >
> >
> >
> >
> > Taufik Al-Sarraj wrote:
> >> Hi,
> >>
> >> Is it possible to have a distance restraint (fix a bond or two)
> >> during a minimization?
> >>
> >> Here is my input file
> >>
> >> CEBP minimization of 20,000 steps
> >> &cntrl
> >> imin = 1,
> >> maxcyc = 20000,
> >> ncyc = 10000,
> >> ntb = 1,
> >> ntr = 0,
> >> cut = 10
> >> /
> >>
> >> The two atoms that should be 2.5A apart are (from the pdb file)
> >> ATOM 1178 ND2 ASN 69 51.852 28.333 61.013
> >> ATOM 2171 O4 T 121 50.434 30.678 61.471
> >>
> >> I am just not sure how to write the restraint.
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> >
>

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