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From: Marios Philippopoulos <mphilip_at_sickkids.on.ca>

Date: Wed 08 Mar 2000 14:13:12 -0500

Hi Vickie,

Just a clarification. Would the following restrained dynamics input file work?

Suppose I am imposing a single restraint between atoms 3 and 5:

&cntrl

imin=0, irest=1, ntx=7,.......,

.........,

&end

&rst iat=3, 5, r1=..., r2=..., r3=..., r4=...,

.........

&end

I guess my question is whether I can put the restraint information right after

the dynamics information in an input file, as i did above. Also do the atom

numbers 3 and 5 correspond to the order of atoms in the topology file? From your

last message I gather they do.

Thanks,

Marios Philippopoulos

Vickie Tsui wrote:

*> > Interesting, but in wich way is it possible to apply an harmonic
*

*> > function to all bonds starting from a PDB file (without dg file) (I beg
*

*> > aprdon if this is a trivial question)?
*

*>
*

*> Because the restraints input into AMBER are specified by the atom numbers
*

*> (see section 4 of Sander), you can write a simple script that will go down
*

*> the PDB file, take the atom numbers corresponding to the atom pairs for
*

*> which you'd like distance restraints from the PDB file (that would give
*

*> you the "IAT" variables). You can also calculate the distance between
*

*> those atoms from the coordinates in the PDB file, and that would determine
*

*> your "r2" and "r3" variables. Then the script can output those
*

*> information (plus your desired r1, r4, and force constants) out in the
*

*> format used for AMBER input restraints. You can do this for all atom
*

*> pairs if you choose (that will give you a huge amount of restraints,
*

*> depending on the size of your system), or for specified groups of the
*

*> molecule.
*

*>
*

*> vickie
*

*>
*

*> The Scripps Research Institute
*

*> 10550 North Torrey Pines Road, TPC-15
*

*> La Jolla, CA 92037
*

*>
*

*> TEL: (858)784-9788
*

*> FAX: (858)784-8896
*

*>
*

*> On Wed, 8 Mar 2000, Andrea Bernini wrote:
*

*>
*

*> > Vickie Tsui wrote:
*

*> > >
*

*> > > You could use distance restraints provided as part of the NMR refinement
*

*> > > utilities to impose harmonic restraints on inter-atomic distances. Right
*

*> > > now the penalty function is such that you can enter r1, r2, r3, r4 values.
*

*> > > If R is the current distance, then the penalty function is:
*

*> > >
*

*> > > R < r1 linear
*

*> > > r1 <= R < r2 parabolic
*

*> > > r2 <= R < r3 Epenalty = 0
*

*> > > r3 <= R < r4 parabolic
*

*> > > r4 <= R linear
*

*> > >
*

*> > > If you want a purely harmonic function, set r1 to 0, r2=r3, and r4 to a
*

*> > > large number, and that should work.
*

*> > >
*

*> > > vickie
*

*> >
*

Date: Wed 08 Mar 2000 14:13:12 -0500

Hi Vickie,

Just a clarification. Would the following restrained dynamics input file work?

Suppose I am imposing a single restraint between atoms 3 and 5:

&cntrl

imin=0, irest=1, ntx=7,.......,

.........,

&end

&rst iat=3, 5, r1=..., r2=..., r3=..., r4=...,

.........

&end

I guess my question is whether I can put the restraint information right after

the dynamics information in an input file, as i did above. Also do the atom

numbers 3 and 5 correspond to the order of atoms in the topology file? From your

last message I gather they do.

Thanks,

Marios Philippopoulos

Vickie Tsui wrote:

-- Marios Philippopoulos, PhD Structural Biology and Biochemistry Programme Hospital for Sick Children 555 University Avenue Toronto Ontario Canada M5G 1X8 mphilip_at_sickkids.on.caReceived on Wed Mar 08 2000 - 11:13:12 PST

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