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 Wed Dec 17 2008 - 01:21:59 PST
