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<DIV><FONT face=Arial size=2><FONT face="Times New Roman" size=3>I just tried
again with another PDB file and it seems to work with the other PDB file?<BR>I
wonder if it just something wrong with the alanin file that I have? Does
anyone else have problems with alanin.pdb?<BR>The alanin.pdb file I am using is
below:<BR><BR>REMARK
FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PDB"<BR>REMARK PARAM11.PRO
( from PARAM6A )<BR>REMARK ===========<BR>REMARK PROTEIN PARAMETERS:<BR>REMARK
PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)<BR>REMARK TORSIONS
FROM HAGLER ET AL JACS 98:4600 (1976)<BR>REMARK LENNARD-JONES NONBONDED
PARAMETERS WITH SPECIAL TREATMENT OF 1:4<BR>REMARK CARBON-CARBON INTERACTIONS:
JORGENSON ET. AL.<BR>REMARK JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1<BR>REMARK
DATE:16-Feb-89 11:21:32 created by user: nonella<BR>ATOM 1 CA ACE 1 -2.184 0.591
0.910 0.0 10.0 MAIN<BR>ATOM 2 C ACE 1 -0.665 0.627 0.966 100.0 0.0 MAIN<BR>ATOM
3 O ACE 1 -0.069 1.213 1.868 100.0 0.0 MAIN<BR>ATOM 4 N ALA 2 0.000 0.000 0.000
100.0 0.0 MAIN<BR>ATOM 5 H ALA 2 -0.490 -0.462 -0.712 100.0 0.0 MAIN<BR>ATOM 6
CA ALA 2 1.450 0.000 0.000 0.0 10.0 MAIN<BR>ATOM 7 CB ALA 2 1.969 -0.670 -1.262
100.0 0.0 MAIN<BR>ATOM 8 C ALA 2 2.010 1.413 0.000 100.0 0.0 MAIN<BR>ATOM 9 O
ALA 2 2.911 1.748 0.767 100.0 0.0 MAIN<BR>ATOM 10 N ALA 3 1.488 2.280 -0.863
100.0 0.0 MAIN<BR>ATOM 11 H ALA 3 0.770 1.998 -1.467 100.0 0.0 MAIN<BR>ATOM 12
CA ALA 3 1.981 3.643 -0.909 0.0 10.0 MAIN<BR>ATOM 13 CB ALA 3 1.147 4.464 -1.880
100.0 0.0 MAIN<BR>ATOM 14 C ALA 3 1.865 4.326 0.444 100.0 0.0 MAIN<BR>ATOM 15 O
ALA 3 2.801 4.963 0.924 100.0 0.0 MAIN<BR>ATOM 16 N ALA 4 0.710 4.211 1.093
100.0 0.0 MAIN<BR>ATOM 17 H ALA 4 -0.026 3.700 0.697 100.0 0.0 MAIN<BR>ATOM 18
CA ALA 4 0.541 4.841 2.388 0.0 10.0 MAIN<BR>ATOM 19 CB ALA 4 -0.809 4.462 2.976
100.0 0.0 MAIN<BR>ATOM 20 C ALA 4 1.591 4.371 3.381 100.0 0.0 MAIN<BR>ATOM 21 O
ALA 4 2.212 5.167 4.085 100.0 0.0 MAIN<BR>ATOM 22 N ALA 5 1.818 3.063 3.463
100.0 0.0 MAIN<BR>ATOM 23 H ALA 5 1.315 2.443 2.895 100.0 0.0 MAIN<BR>ATOM 24 CA
ALA 5 2.809 2.556 4.392 0.0 10.0 MAIN<BR>ATOM 25 CB ALA 5 2.970 1.055 4.209
100.0 0.0 MAIN<BR>ATOM 26 C ALA 5 4.176 3.170 4.142 100.0 0.0 MAIN<BR>ATOM 27 O
ALA 5 4.859 3.615 5.064 100.0 0.0 MAIN<BR>ATOM 28 N ALA 6 4.611 3.212 2.886
100.0 0.0 MAIN<BR>ATOM 29 H ALA 6 4.055 2.853 2.163 100.0 0.0 MAIN<BR>ATOM 30 CA
ALA 6 5.908 3.786 2.586 0.0 10.0 MAIN<BR>ATOM 31 CB ALA 6 6.121 3.830 1.082
100.0 0.0 MAIN<BR>ATOM 32 C ALA 6 6.012 5.221 3.079 100.0 0.0 MAIN<BR>ATOM 33 O
ALA 6 6.992 5.614 3.710 100.0 0.0 MAIN<BR>ATOM 34 N ALA 7 5.002 6.040 2.802
100.0 0.0 MAIN<BR>ATOM 35 H ALA 7 4.228 5.711 2.297 100.0 0.0 MAIN<BR>ATOM 36 CA
ALA 7 5.044 7.419 3.245 0.0 10.0 MAIN<BR>ATOM 37 CB ALA 7 3.730 8.110 2.918
100.0 0.0 MAIN<BR>ATOM 38 C ALA 7 5.219 7.518 4.752 100.0 0.0 MAIN<BR>ATOM 39 O
ALA 7 6.045 8.278 5.255 100.0 0.0 MAIN<BR>ATOM 40 N ALA 8 4.445 6.748 5.512
100.0 0.0 MAIN<BR>ATOM 41 H ALA 8 3.792 6.148 5.096 100.0 0.0 MAIN<BR>ATOM 42 CA
ALA 8 4.566 6.799 6.956 0.0 10.0 MAIN<BR>ATOM 43 CB ALA 8 3.670 5.747 7.589
100.0 0.0 MAIN<BR>ATOM 44 C ALA 8 5.984 6.488 7.409 100.0 0.0 MAIN<BR>ATOM 45 O
ALA 8 6.560 7.186 8.241 100.0 0.0 MAIN<BR>ATOM 46 N ALA 9 6.582 5.429 6.871
100.0 0.0 MAIN<BR>ATOM 47 H ALA 9 6.109 4.882 6.209 100.0 0.0 MAIN<BR>ATOM 48 CA
ALA 9 7.934 5.082 7.264 0.0 10.0 MAIN<BR>ATOM 49 CB ALA 9 8.436 3.918 6.425
100.0 0.0 MAIN<BR>ATOM 50 C ALA 9 8.898 6.233 7.027 100.0 0.0 MAIN<BR>ATOM 51 O
ALA 9 9.705 6.584 7.887 100.0 0.0 MAIN<BR>ATOM 52 N ALA 10 8.839 6.851 5.851
100.0 0.0 MAIN<BR>ATOM 53 H ALA 10 8.190 6.560 5.176 100.0 0.0 MAIN<BR>ATOM 54
CA ALA 10 9.733 7.956 5.567 0.0 10.0 MAIN<BR>ATOM 55 CB ALA 10 9.388 8.570 4.219
100.0 0.0 MAIN<BR>ATOM 56 C ALA 10 9.595 9.067 6.595 100.0 0.0 MAIN<BR>ATOM 57 O
ALA 10 10.580 9.587 7.117 100.0 0.0 MAIN<BR>ATOM 58 N ALA 11 8.364 9.460 6.912
100.0 0.0 MAIN<BR>ATOM 59 H ALA 11 7.590 9.036 6.488 100.0 0.0 MAIN<BR>ATOM 60
CA ALA 11 8.169 10.516 7.887 0.0 10.0 MAIN<BR>ATOM 61 CB ALA 11 6.686 10.695
8.168 100.0 0.0 MAIN<BR>ATOM 62 C ALA 11 8.823 10.177 9.217 100.0 0.0
MAIN<BR>ATOM 63 O ALA 11 9.523 10.992 9.815 100.0 0.0 MAIN<BR>ATOM 64 N CBX 12
8.610 8.962 9.714 100.0 0.0 MAIN<BR>ATOM 65 H CBX 12 8.050 8.324 9.225 100.0 0.0
MAIN<BR>ATOM 66 CA CBX 12 9.223 8.571 11.014 0.0 10.0 MAIN<BR>END<BR><BR>-----
Original Message ----- <BR>From: Shirley Hui<BR>To: </FONT><A
href="mailto:mmtk@python.net"><FONT face="Times New Roman"
size=3>mmtk@python.net</FONT></A><BR><FONT face="Times New Roman" size=3>Sent:
Monday, May 10, 2004 7:51 PM<BR>Subject: [MMTK] PDB file<BR><BR><BR>I am trying
to read in a PDB fille.<BR>My code looks like this:<BR>from MMTK import
*<BR>from MMTK.PDB import PDBConfiguration<BR>from MMTK.ForceFields import
Amber94ForceField<BR>import sys<BR>conf =
PDBConfiguration('alanin.pdb')<BR>chains =
conf.createPeptideChains()<BR>universe =
InfiniteUniverse(Amber94ForceField())<BR>universe.addObject(chains)<BR>print
universe.energy()<BR>print universe.energyTerms()['electrostatic']<BR>When I try
and specify the PDB file to be something that was not included in<BR>the source
distribution (i.e. a configuration that is not 2YCC.pdb,<BR>insulin.pdb etc), I
get errors. For example, I got alanin.pdb from the<BR>protein
databank. I put this file
in<BR>C:\Python23\Lib\site-packages\MMTK\Database\PDB. When I run the code
as<BR>above, I get the following error:<BR>Traceback (most recent call
last):<BR>
File<BR>"C:\PYTHON23\lib\site-packages\Pythonwin\pywin\framework\scriptutils.py",<BR>line
310, in RunScript<BR> exec codeObject in
__main__.__dict__<BR> File "C:\Python23\Scripts\shirl.py", line 6, in
?<BR><BR> File "c:\python23\Lib\site-packages\MMTK\PDB.py", line 147, in
__init__<BR> Scientific.IO.PDB.Structure.__init__(self,
filename)<BR> File "C:\PYTHON23\Lib\site-packages\Scientific\IO\PDB.py",
line 890, in<BR>__init__<BR>
self.parseFile(PDBFile(filename))<BR> File
"C:\PYTHON23\Lib\site-packages\Scientific\IO\PDB.py", line 1041,
in<BR>parseFile<BR> type, data = file.readLine()<BR>
File "C:\PYTHON23\Lib\site-packages\Scientific\IO\PDB.py", line 152,
in<BR>readLine<BR> data = {'serial_number': line[1],<BR>
File "C:\PYTHON23\Lib\site-packages\Scientific\IO\FortranFormat.py",
line<BR>122, in __getitem__<BR> return
self.data[i]<BR>IndexError: list index out of range<BR>If instead I have
insulin.pdb instead of alanin.pdb, it works.<BR>Is there something I am doing
wrong? I even created an evironment variable<BR>in my PATH called MMTKPATH
according to this link:<BR></FONT><A
href="http://starship.python.net/crew/hinsen/mmtk_manual/database.html"><FONT
face="Times New Roman"
size=3>http://starship.python.net/crew/hinsen/mmtk_manual/database.html</FONT></A><BR><FONT
face="Times New Roman" size=3>I tried setting this env variable to
be:<BR>C:\Python23\Lib\site-packages\MMTK\Database\PDB
and<BR>C:\Python23\Lib\site-packages\MMTK\Database, but neither
work??<BR><BR>Thanks in
advance,<BR>shirley<BR><BR><BR><BR><BR>_______________________________________________<BR>mmtk
maillist - </FONT><A href="mailto:mmtk@starship.python.net"><FONT
face="Times New Roman" size=3>mmtk@starship.python.net</FONT></A><BR><A
href="http://starship.python.net/mailman/listinfo/mmtk"><FONT
face="Times New Roman"
size=3>http://starship.python.net/mailman/listinfo/mmtk</FONT></A><BR></FONT></DIV></BODY></HTML>