AMBER Archive (2008)

Subject: Re: AMBER: distance restraint in minimization

From: luzhenw1_at_msu.edu
Date: Wed Dec 17 2008 - 09:10:49 CST


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

¬†¬†ŚľēÁĒ® "Taufik Al-Sarraj" <taufik.alsarraj_at_utoronto.ca>Ôľö

> 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_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>     to majordomo_at_scripps.edu
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>      to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu