AMBER Archive (2008)

Subject: Re: AMBER: distance restraint in minimization

From: Jifeng Wang (wangjf_at_gmail.com)
Date: Wed Dec 17 2008 - 12:16:08 CST

Hi, Taufik,
To recompile,
1. >cd */amber10/src/nmr_aux/prepare_input/
2. >make clean
3. >make
4. >make install

You will notice some new executables created in exe folder and new map*
created in dat folder. (though the latters are the same as before).

Good luck,
Jifeng
On Wed, Dec 17, 2008 at 12:44 PM, Taufik Al-Sarraj <
taufik.alsarraj_at_utoronto.ca> wrote:

> 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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