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.
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Received on Fri Dec 19 2008 - 01:08:58 PST
