AMBER Archive (2008)

Subject: Re: AMBER: distance restraint between non-bonded molecules

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Dec 18 2008 - 15:29:26 CST

I tend not to use the scripts that come with AMBER if the system is easy
to create/analyze. In your case, I guess you have only 4 distance
restraints, is that right? If that is the case, try doing the following:

1. Create a .pdb file using the prmtop/inpcrd files of the simulation you
are intended to do. This .pdb file will order the atoms according to
prmtop file. This is a very crucial step!

2. Find which atoms are going to be restrained. For instance, for the
first restraint, you had :11_at_ND2 - :142_at_DT distance restrained. Find those
atoms. You will use the corresponding atom numbers of these atoms in the
.pdb file while creating the RST file.

3. Create the lines in your RST file using the atom numbers found in step
# 2. As an example, look at the following entry:

---------------
# 1 RA5 1H6 14 RU3 O4 1.34 2.34
 &rst
  ixpk= 0, nxpk= 0, iat= 18, 431, r1= 0.84, r2= 1.34, r3= 2.34, r4=
2.84,
      rk2=25.0, rk3=25.0, ir6=1, ialtd=0,
 &end
#
-----------------

In this entry, the atoms of 18 and 431 (iat=18,431) are restrained. The
force constant used in this restraint is 25 kcal/molA^2. Check out the
manual to get an idea on the other parameters.

4. Create the other entries in the RST file, but do not include the
rk2,rk3,ir6,ialtd terms in the entries (the first entry has all the
necessary information; so you do not need to include them in the next
entries unless you want to change the force constants of particular
distance restraints).

If you do everything right, it should work in your simulations. I am not
sure why you have igr1 defined in your RST entries. If only 2 atoms are
going to be restrained, you do not need to use igr1. It is to define a
group of atoms (I think). Are you planning to use distance restraints in a
group of atoms? In the above steps, I assumed that 2 particular atoms are
going to have distance restraints.

Hope this helps. Good luck.

On Thu, 18 Dec 2008, Taufik Al-Sarraj wrote:

> Hi Ilyas,
> Thank you for noticing this. I did some experimenting, if i change 11
> ASN ND2 to something like 10 ARG CD i get
> # 10 ARG CD 143 DT O4 5.0 5.5
> &rst
> ixpk= 0, nxpk= 0, iat= 156,2870, r1= 4.50, r2= 5.00, r3= 5.50, r4=
> 6.00, &end
> #
>
> so the iat looks good. I looked at
> /usr/local/Programs/amber10.09/dat/map.DG-AMBER and i noticed that ASN
> ND2 has two atoms next to it. Could that be the reason?
>
> RESIDUE ASN
> MAPPING ND2 = HD21 HD22
>
>
> I also tried ASN N only and i got iat numbers that make sense
>
> Thank you,
> Taufik
>
> Ilyas Yildirim wrote:
> >> the RST file is
> >> #
> >> # 11 ASN ND2 142 DT O4 2.5
> >> &rst
> >> ixpk= 0, nxpk= 0, iat= -1,2838, r1= 1.30, r2= 1.80, r3= 2.81, r4= 3.31,
> >>
> >> rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
> >> igr1= 180, 181,
> >> &end
> >> #
> >> # 11 ASN ND2 143 DT O4 5.5
> >> &rst
> >> ixpk= 0, nxpk= 0, iat= -1,2870, r1= 1.30, r2= 1.80, r3= 6.17, r4= 6.67,
> >> igr1= 180, 181,
> >> &end
> >> #
> >> # 69 ASN ND2 121 DT O4 2.5
> >> &rst
> >> ixpk= 0, nxpk= 0, iat= -1,2171, r1= 1.30, r2= 1.80, r3= 2.81, r4= 3.31,
> >> igr1=1179,1180,
> >> &end
> >> #
> >> # 69 ASN ND2 122 DT O4 5.5
> >> &rst
> >> ixpk= 0, nxpk= 0, iat= -1,2203, r1= 1.30, r2= 1.80, r3= 6.17, r4= 6.67,
> >> igr1=1179,1180,
> >> &end
> >>
> >
> > The atoms that are restrained in the first case are atom number -1 and and
> > atom number 2838. This does not look so normal. It should be a positive
> > number. Generally I re-create the .pdb using the prmtop/inpcrd files, and
> > then use that .pdb file to create the RST file.
> >
> >
>
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-- 
  Ilyas Yildirim, Ph.D.
  ---------------------------------------------------------------
  = Hutchison Hall B#10          - Department of Chemistry      =
  =                              - University of Rochester      =
  = 585-275-6766 (office)        -                              =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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