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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear all,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>I have two question:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>1) Are the atom types I chose for the use of OPLS
force field correct?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>I use gromacs 4.0.7 with opls force field under
Ubuntu Linux to simulate enzyme drug interaction. Since the Dundee Prodrg
Server converts PDB files of drug structures just in an .itp file compatible
with gromos forcefields, I had to change the atom types as follows:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>drug.itp:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'> [ moleculetype ]<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>; Name nrexcl<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>drug 3<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>[ atoms ]<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>; nr
type resnr resid atom cgnr
charge mass<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>
1 opls_145
1 DRG C1 1
-0.018 13.0190 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 2 opls_729
1 DRG C2
1 0.002 12.0110 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 3
opls_730 1 DRG
BR1 1 0.016 79.9040
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>
4 opls_166
1 DRG C3
2 0.149 12.0110 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 5
opls_167 1 DRG
O1 2 -0.174 15.9994 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>
6 opls_168
1 DRG HAA 2
0.066 1.0080 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 7
opls_145 1 DRG
C4 2 -0.020 13.0190 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>
8 opls_145
1 DRG C5 2
-0.021 13.0190 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 9
opls_145 1 DRG
C6 3 0.002 12.0110 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 10
opls_136 1 DRG
C7 3 0.093 14.0270 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 11
opls_139 1 DRG
C8 3 0.172 12.0110 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 12
opls_750 1 DRG
N1 3 -0.267 14.0067 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 13 opls_154
1 DRG O2 4
-0.108 15.9994 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>
14 opls_155
1 DRG HAB 4
0.108 1.0080 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 15
opls_235 1 DRG
C9 5 0.395 12.0110 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>
16
opls_236 1 DRG
O3 5 -0.664 15.9994 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font><font size=2 face=Arial><span
lang=EN-GB style='font-size:10.0pt;font-family:Arial'>17
opls_237 1 DRG
N2 5 0.159 14.0067 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>
18
opls_240 1 DRG
HAD 5 0.024
1.0080 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>
19
opls_136 1 DRG
C10 5 0.086 14.0270
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>
20
opls_206 1 DRG
C11 6 0.000 14.0270
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>
21
opls_083 1 DRG
S1 7 -1.000 32.0600 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Drug.gro:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>PRODRG COORDS<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'> 21<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'> 1DRG
C1 1 8.555
5.270 -3.838<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'> 1DRG
C2 2 8.529
5.317 -3.967<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'> 1DRG
BR1 3 8.392 5.231
-4.068<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
C3 4 8.602
5.424 -4.019<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
O1 5 8.580
5.472 -4.145<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
HAA 6 8.507 5.419
-4.189<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
C4 7 8.700
5.485 -3.941<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
C5 8 8.725
5.438 -3.812<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
C6 9 8.653
5.331 -3.760<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
C7 10 8.681 5.281
-3.619<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
C8 11 8.788 5.172
-3.616<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
N1 12 8.913 5.205
-3.598<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
O2 13 8.945 5.341
-3.583<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG HAB
14 9.044 5.351 -3.570<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
C9 15 8.736 5.032
-3.632<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font><font size=2 face=Arial><span
lang=EN-GB style='font-size:10.0pt;font-family:Arial'>1DRG
O3 16 8.619 5.004
-3.652<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'> 1DRG
N2 17 8.828 4.932
-3.624<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'> 1DRG
HAD 18 8.925 4.956 -3.626<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'> </span></font><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>1DRG
C10 19 8.790 4.792 -3.610<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG C11
20 8.903 4.690 -3.629<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> 1DRG
S1 21 8.838 4.520
-3.654<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font><font size=2 face=Arial><span
lang=EN-GB style='font-size:10.0pt;font-family:Arial'>1.11480
1.11480 1.11480<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>2) Visualization problem of VMD? <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>The second question is related to the first one:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>I use VMD 1.8.7 under Windows XP. When I try to
visualize above mentioned Drg.gro file using VMD, the bromo atom appears as a
tiny point and is not connected to C2 as it should. When I convert the Drg.gro
file to a pdf-file by the command editconf, the pdf-structure displays the
bromo atom correctly connected to the aromatic ring. In addition, during the
course of an mdrun over 1 ns the relative position and the distance of the
bromo atom to C2 remained unchanged. The distance between BR1 and C2 in the
final mdrun after some relaxation was constantly 1.89 Angstrom which is
realistic. Is my observation a visualization problem of VMD or a serious
problem with gromacs which I do not see.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>If it is a problem with VMD, Is there a remedy for
the incorrect visualization of the drug molecule?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Thank you in advance,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Franz<o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>F.-J. Meyer-Almes<o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>Hochschule
Darmstadt<o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>Fachbereich Chemie-
und Biotechnologie<o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>Schnittspahnstr. 12<o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>64287 Darmstadt<o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>Email:
franz-josef.meyer-almes@h-da.de<o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>Tel.: ++49-(0)6151-168406<o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;line-height:14.0pt'><font size=1
face=Arial><span style='font-size:8.0pt;font-family:Arial'><a
href="http://www2.h-da.de/cub/index.php?id=177">http://www2.h-da.de/cub/index.php?id=177</a></span></font><font
size=1 face=Arial><span style='font-size:8.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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