JIfeng is going to answer your second.
For the first one, ' ERROR no map function for O4 T :data= 11 ASN ND2 142 T O4 2.5'. it seems to me that the name is not defined in the map. My way to fix it is just modify the map (map.DG-AMBER ) and use makeDIST_RST -map option to load the modified map. it works for me at least.
zhenwei
zhenwei
( 引用 "Taufik Al-Sarraj" <taufik.alsarraj.utoronto.ca>：
> 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.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.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.
>>>> -----------------------------------------------------------------------
>>>> The AMBER Mail Reflector
>>>> To post, send mail to amber.scripps.edu
>>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>>> to majordomo.scripps.edu
>>>
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber.scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>> to majordomo.scripps.edu
>>>
>>>
>>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Dec 19 2008 - 01:10:56 PST
