X-plor questions

Brian Marsden marsden at bioch.ox.ac.uk
Thu Jan 29 05:04:14 EST 1998

Tina Marie Conti wrote:

> I am very new to x-plor so the following questions may seem quite basic
> but any help is greatly appreciated.
> 1)  I am trying to set up PICK statements to get an output of specified
> dihedral angles.  The statement I set up looks like:
>         (atom 1)
>         (atom 2)
>         (atom 3)
>         (atom 4)
>         geometry
> The same lines appear in the log file but the angle is not listed.  I
> assume maybe I need a print statement but have no idea how to set it up.
> Any help?

Are the atoms in the right order? For example:

pick dihedral (resid 2 and name C)(resid 2 and name CA)
	      (resid 2 and name N)(resid 1 and name C) geometry

is wrong but

pick dihedral (resid 1 and name C)(resid 2 and name N)
	      (resid 2 and name CA)(resid 2 and name C) geometry

is right.

Make sure that you remove all the set messages=off echo=off end
statements so that you can see if the dihedral is being picked properly.
A typical output is like this:

 X-PLOR>pick dihedral (resid 1237 and name C)(resid 1238 and name N) 
 SELRPN:      1 atoms have been selected out of   2798
 SELRPN:      1 atoms have been selected out of   2798
 SELRPN>              (resid 1238 and name CA)(resid 1238 and name C)
 SELRPN:      1 atoms have been selected out of   2798
 SELRPN:      1 atoms have been selected out of   2798
 GEOM=    -74.917092

> 2)  I have 5 print statements set up for various parameters.  All seem to
> work except the one that prints cdih violations (the syntax follows the
> statements that work so I don't really know what the problem is).  I have
> set the threshold to zero and I still do not get any violations (although
> when I measure the angles manually, most are significantly different from
> the input equilibrium angle).  Any ideas? (I should mention that the file
> listing the dihedral angle restraints is read without error, but the
> E(cdih) value is consistenly zero, and I have included cdih in the flag
> statement).

If E(CDIH)=0 then one of two things is possible: Your restraints are not
being read in properly (even though you say there are no errors - again,
remove the set messages e.t.c. commands to be sure) or you have set the
weight for CDIH to be 0 (with the constraints interaction weights

> 3)  This last question may be too much to answer without my input file but
> here it is:  The energy minimization never converges.  I have set nsteps
> to 3000 and the lowest grad I have gotten is around 0.18.  I have tried
> breaking down the minimization into 10 x 200 (for example) as was
> suggested previously but there is still no convergence.  Any ideas?

Sounds like not all of the atoms are free - i.e. some are fixed in
space. Breaking up the minimization will not make any difference (in my
experience). Bit difficult to help here without seeing the full script.

> Again, I appreciate any help and apologize if the questions are
> simplistic.

Well I hope this has helped a bit.



 Brian Marsden    marsden at bioch.ox.ac.uk       Home: +44 1865 552696	
 OCMS, Oxford     Fax: +44 1865 275253	       Work: +44 1865 275720

More information about the X-plor mailing list