Dear Carlos,
Thank you for your help. I have gone through the manual
and could understand the restraint energy functions. But I am facing some
problems. First of all I have changed to ialtd=1 instead of ialtd=0 since it
gives a stiffer value (hyperbolic rather than linear) beyond r4. Now as far
I could understand We can restrain the distance by either monitoring r1->r4
values or maximizing rk2 and rk3 values. Since my restrained value is very
low of around 1.8 A there is low probability of the distance coming to lower
value during MD. So if I keep the rst.dist files like bellow
&rst
ixpk= 0, nxpk= 0, iat= 1735, 2946, r1= 0.1, r2= 0.3, r3= 1.8, r4= 2.3,
rk2=0.0, rk3=2000.0, ir6=1, ialtd=1,
&end
By either giving high rk3 value (as shown above) or by giving high r4 value
I can keep the distance constrained in the desired value of around 1.8A.
This was fine with the minimization protocol (both minimization constraining
the solute as well as the whole system). But I am unable to run the
equilibrium run with this. During equilibration (where I am inceresing the
temperature from 100K to 300K) we are unable to give very high rk3 value as
it is showing problem with SHAKE where vlimit exceed. Neither giving very
high value to r4 provides a desired result i.e. I am unable to restrain the
desired distance. I am confused what should I do next. Kindly suggest some
solution.
On Mon, Apr 18, 2011 at 9:33 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I don't think you should use the script- what you were doing before was
> fine
> but you need to adjust the values of r1, r2, r3 and r4. the first step is
> to
> read and understand what the form of the restraint energy function looks
> like. then you can understand the forces at each of these values- you will
> not be able to understand how to set the r values until you learn about the
> restraint function. ask back here after reading if you have specific
> questions.
>
>
> On Mon, Apr 18, 2011 at 9:29 AM, nicholus bhattacharjee <
> nicholusbhattacharjee.gmail.com> wrote:
>
> > 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)
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Nicholus Bhattacharjee
> > PhD Scholar
> > Department of Chemistry
> > University of Delhi
> > Delhi-110007 (INDIA)
> > Phone: 9873098743(M)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Thu Apr 21 2011 - 22:30:06 PDT
