Can you send me your prmtop/inpcrd and RST files?
On Fri, 19 Dec 2008, Taufik Al-Sarraj wrote:
> Hi Ilyas,
>
> Thank you for all the details. I tried what you suggested. I think AMBER
> treats this specific Nitrogen (ASN ND2) as a group. I took the RST file
> and modified the -1 to the atom number of the nitrogen only and i ran
> the simulation. I noticed that the results were very similar.
>
> Thank you again,
> Taufik
>
>
> Ilyas Yildirim wrote:
> > 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.ND2 - :142.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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> >>
> >>
> >>
> >
> >
>
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>
--
Ilyas Yildirim, Ph.D.
---------------------------------------------------------------
= Hutchison Hall B#10 - Department of Chemistry =
= - University of Rochester =
= 585-275-6766 (office) - =
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Received on Fri Dec 19 2008 - 18:43:16 PST
