AMBER Archive (2008)

Subject: Re: AMBER: distance restraint in minimization

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Tue Dec 16 2008 - 15:16:43 CST

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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