Dear Carlos,
Thank you for the suggestion. Since it is written in the
manual that we can use of makeDIST_RST program to generate rst.dist I
thought of using that. As my protein is very large one I thought of cutting
it down to the portion where the distance of interest is there. Then with
the help of leap I have generated the prmtop and inpcrd files and then
generated pdb file from them. The pdb file is as bellow
filename: y
REMARK
ATOM 1 N GLY 1 22.187 33.466 34.876
ATOM 2 H1 GLY 1 22.612 34.340 35.151
ATOM 3 H2 GLY 1 22.918 32.811 34.635
ATOM 4 H3 GLY 1 21.489 33.214 35.561
ATOM 5 CA GLY 1 21.449 33.691 33.640
ATOM 6 2HA GLY 1 21.855 33.033 32.872
ATOM 7 3HA GLY 1 20.402 33.442 33.814
ATOM 8 C GLY 1 21.543 35.144 33.153
ATOM 9 O GLY 1 20.509 35.779 32.929
ATOM 10 N VAL 2 22.795 35.660 33.010
ATOM 11 H VAL 2 23.537 34.977 33.072
ATOM 12 CA VAL 2 23.138 37.035 32.556
ATOM 13 HA VAL 2 23.813 37.891 32.546
ATOM 14 CB VAL 2 25.757 33.019 32.799
ATOM 15 HB VAL 2 25.448 32.833 33.827
ATOM 16 CG1 VAL 2 25.963 31.691 32.083
ATOM 17 1HG1 VAL 2 26.273 31.876 31.055
ATOM 18 2HG1 VAL 2 26.734 31.117 32.596
ATOM 19 3HG1 VAL 2 25.030 31.128 32.085
ATOM 20 CG2 VAL 2 25.377 36.759 33.724
ATOM 21 1HG2 VAL 2 24.471 36.898 34.315
ATOM 22 2HG2 VAL 2 26.242 37.080 34.305
ATOM 23 3HG2 VAL 2 25.311 37.354 32.813
ATOM 24 C VAL 2 22.473 37.379 31.220
ATOM 25 O VAL 2 22.131 36.451 30.482
ATOM 26 N ALA 3 22.323 38.699 30.907
ATOM 27 H ALA 3 22.579 39.375 31.613
ATOM 28 CA ALA 3 21.640 39.184 29.685
ATOM 29 HA ALA 3 20.715 38.614 29.773
ATOM 30 CB ALA 3 21.307 40.660 29.757
ATOM 31 1HB ALA 3 22.222 41.245 29.661
ATOM 32 2HB ALA 3 20.625 40.919 28.947
ATOM 33 3HB ALA 3 20.834 40.880 30.714
ATOM 34 C ALA 3 22.252 38.888 28.329
ATOM 35 O ALA 3 23.387 39.292 28.057
ATOM 36 OXT ALA 3 21.698 38.116 27.550
TER
ATOM 37 O WAT 4 27.645 31.432 29.113
ATOM 38 H1 WAT 4 28.602 31.432 29.113
ATOM 39 H2 WAT 4 27.405 32.359 29.113
TER
ATOM 40 O WAT 5 25.601 32.128 31.177
ATOM 41 H1 WAT 5 26.558 32.128 31.177
ATOM 42 H2 WAT 5 25.361 33.055 31.177
TER
ATOM 43 O WAT 6 26.428 40.731 28.774
ATOM 44 H1 WAT 6 27.385 40.731 28.774
ATOM 45 H2 WAT 6 26.188 41.658 28.774
TER
END
The atoms of interest are 2-VAL-CB and 5-WAT-O with distance between them
1.85717666 A. Now as suggested by tutorial
http://ambermd.org/tutorials/advanced/tutorial4/ I have prepared a 7col.dist
file as bellow
filename: 7col.dist
2 VAL CB 5 WAT O 1.8
Now when I use makeDIST_RST following errors are coming
$ makeDIST_RST -upb 7col.dist -pdb y -rst rst.dist
# makeDIST_RST
Currently configured for up to 5000 atoms
Using MAP file /usr/local/amber9/dat/map.DG-AMBER
ERROR no map function for CB VAL :data= 2 VAL CB 5 WAT
O 1.8
I am not understanding the problem. Thank you for your help.
On Mon, Apr 18, 2011 at 4:42 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Your usage of r1 and r4 are not correct. Look closely at the manual. You
> have defined a flat restraint. Move those values away from the harmonic
> part
> of the potential. Read the details in manual carefully to understand the
> function being used.
>
> On Apr 18, 2011 5:46 AM, "nicholus bhattacharjee" <
> nicholusbhattacharjee.gmail.com> wrote:
>
> Dear community,
> I am running simulation of a protein which
> contains water molecules in its pdb file. I have prepared topology and
> coordinate files by retaining the water molecules present in the pdb file.
> By regenerating the pdb file with the help of ambpdb the protein atom and
> water molecule oxygen atom numbers and distance in which I am interested
> are
> 1735, 2946 and 1.85717666 A respectively. So I prepared the following file
> to keep the distance between this two atoms constant
>
> filename: rst.dst
> #
> # Change in distance
> &rst
> ixpk= 0, nxpk= 0, iat= 1735, 2946, r1= 1.85717666, r2= 1.85717666, r3=
> 1.85717666, r4= 1.85717666,
> rk2=0.0, rk3=320.0, ir6=1, ialtd=0,
> &end
>
> My input file for minimization of only the water molecules is as bellow
>
> filename: min.in
> minimisation with solute restrain
> &cntrl
> imin=1,maxcyc=500,ncyc=250
> ntpr=5,ntr=1, nmropt=1,
> restraint_wt=1000.0
> restraintmask=':1-164', #my protein contains 164 residues
> /
> &wt type='END' /
> DISANG=rst.dist
>
>
> But after minimization is over the atoms of interest (numer: 1735 and 2946)
> are not remaining in the same distance. I am not able to understand where I
> am going wrong. Please help. Thank you in advance.
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
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>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Mon Apr 18 2011 - 07:00:02 PDT
