AMBER Archive (2008)

Subject: Re: AMBER: distance restraint in minimization

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Dec 17 2008 - 11:44:55 CST

Hi Zhenwei,
I am a little confused actually. For the second point i modified the pdb
file and it seems that the RST.f file is similar to the one on page
192-3 of the manual and similar to the one on
http://www.uni-koeln.de/themen/Chemie/software/amber7/tutorial/dna_NMR/nmr_dna_tutorial.htm.
I was hoping that is correct.

For the first point, I just changed global.h but i have never recompiled
amber before. is it as easy as ./configure_amber and make serial (i am
running this on my local machine for now) I am just a little worried
about missing something like make clean first.

Thank you again,
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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