building .psf and .pdb for a polylys oligo

Eugene Leitl ui22204 at mail.lrz-muenchen.de
Wed Mar 4 06:24:20 EST 1998


Dear X-PLORers,

I am a beginner in the MD field, facing the following problem: a part of
my initial state box is a polylysine chloride oligo (I am to investigate
polycation-induced lateral segregation of lipid anions in the lipid
bilayer). Building coordinate files (pdb) is easy with Corina or the
protein tool from the Tinker suite. Painstakingly, chloride ions can be
added to the pdb file by hand. (I thought some steepest descent
minimization followed by, say, 100 ps of MD should equilibrate the system
well enough for subsequent solvation). With some manual tweaking, it is
possible to hydrate such systems with Solvate (which also generates the
mkspf.inp for TIPS3P's and the stochastic boundary defining files). Btw
Solvate, I have failed to find toph19.nacl param19.nacl in the standard
X-PLOR(online) Version 3.851 distribution? 

However, I still can't make psfs. In my naivete I wrote a script running 
like:

topology  @@TOPPAR:topallhdg.pro end
segment
  name="    "
  chain
     @@TOPPAR:toph19.pep
     sequence
       Lys Lys Lys Lys Lys Lys Lys Lys Lys Lys
       Lys Lys Lys Lys Lys Lys Lys Lys Lys Lys
       Lys Lys Lys Lys Lys Lys Lys Lys Lys Lys
       Lys Lys Lys Lys Lys Lys Lys Lys Lys Lys
       Lys Lys Lys Lys Lys Lys Lys Lys Lys Lys
     end
   end
end
REMARK Polylys 50-mer
write structure output=polylys.psf end
write coordinates output=polylys.pdb end
stop

The psf file seemed fine(?), but the according pdb contained bogus 
coordinates. Unabashed, I substituted the 'sequence end' block with

     coordinates @polylys.pdb

(is there a difference between @ and @@?)

with polylys.pdb containing bona fide coordinates from Tinker's protein 
tool. Alas, the naming of the groups ATOMs belong to seemed to be different:
Tinker:
ATOM      1  N   LYS     1       0.000   0.000   0.000
ATOM      2  CA  LYS     1       0.000   0.000   1.500
ATOM      3  C   LYS     1       1.413   0.000   2.034
ATOM      4  O   LYS     1       1.755   0.688   2.981
ATOM      5  CB  LYS     1      -0.698  -1.273   2.014
ATOM      6  CG  LYS     1      -0.698  -1.273   3.554
ATOM      7  CD  LYS     1      -1.395  -2.546   4.068
ATOM      8  CE  LYS     1      -1.395  -2.546   5.608
ATOM      9  NZ  LYS     1      -2.074  -3.786   6.109

X-PLOR:
ATOM      1  CA  LYS     1    9999.0009999.0009999.000  1.00  0.00
ATOM      2  HA  LYS     1    9999.0009999.0009999.000  1.00  0.00
ATOM      3  CB  LYS     1    9999.0009999.0009999.000  1.00  0.00
ATOM      4  HB1 LYS     1    9999.0009999.0009999.000  1.00  0.00
ATOM      5  HB2 LYS     1    9999.0009999.0009999.000  1.00  0.00
ATOM      6  CG  LYS     1    9999.0009999.0009999.000  1.00  0.00
ATOM      7  HG1 LYS     1    9999.0009999.0009999.000  1.00  0.00
ATOM      8  HG2 LYS     1    9999.0009999.0009999.000  1.00  0.00
ATOM      9  CD  LYS     1    9999.0009999.0009999.000  1.00  0.00

What to do? Should I abandon Tinker, and generate my oligos with X-PLOR? 
If yes, which scripts are of use then, and can they handle chlorides?

Please advice,
Regards,
Eugene Leitl, MSU, Polymer Sci. Dept.





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