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<DIV>Dear GMX'ers,</DIV>
<DIV> Is there any reliable way of making an itp file for an
arbitrary structure? AFAIK there are two ways:</DIV>
<DIV><FONT face=Arial size=2> 1) The Dundee
PRODRG server. This is really a nice tool, but it always gives the same
protonation states. COOH always becomes COO- and NH2 becomes NH3+. </FONT></DIV>
<DIV><FONT face=Arial size=2> 2) x2top.
This utility hangs with my rather simple structure. The structure
is attached below. This is a file created by SwissPDB. It contains
hydrogens and connections. Nevertheless x2top ignores this information and
hanges (at least gives no result in 40 min).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>So, the question is how to make an itp file with
predefined protonation (e.g. COOH and NH2 groups).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Here is a pdb file</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>COMPND
?<BR>REMARK File generated by Swiss-PdbViewer
3.70b15<BR>REMARK <A
href="http://www.expasy.org/spdbv/">http://www.expasy.org/spdbv/</A><BR>HETATM
1 C1 PDR 1
43.433 46.174 18.374 1.00
0.00<BR>HETATM 2 C2 PDR
1 42.232 46.505 18.873
1.00 0.00<BR>HETATM 3 C3
PDR 1 41.148
45.500 19.008 1.00 0.00<BR>HETATM 4
C4 PDR 1
41.322 44.220 18.637 1.00
0.00<BR>HETATM 5 C5 PDR
1 43.713 44.783 17.941
1.00 0.00<BR>HETATM 6 C6
PDR 1 42.617
43.776 18.072 1.00 0.00<BR>HETATM 7
C7 PDR 1
42.814 42.509 17.658 1.00
0.00<BR>HETATM 8 C8 PDR
1 44.112 42.120 17.056
1.00 0.00<BR>HETATM 9 C9
PDR 1 45.096
43.026 16.934 1.00 0.00<BR>HETATM 10 C10
PDR 1 44.906
44.416 17.421 1.00 0.00<BR>HETATM 11 O11
PDR 1 45.923
45.378 17.183 1.00 0.00<BR>HETATM 12 C12
PDR 1 46.990
45.244 18.162 1.00 0.00<BR>HETATM 13 C13
PDR 1 48.059
46.309 17.874 1.00 0.00<BR>HETATM 14 O14
PDR 1 47.658
47.553 18.487 1.00 0.00<BR>HETATM 15 C15
PDR 1 49.462
45.937 18.365 1.00 0.00<BR>HETATM 16 N16
PDR 1 50.433
46.887 17.760 1.00 0.00<BR>HETATM 17 C17
PDR 1 51.853
46.544 17.977 1.00 0.00<BR>HETATM 18 C18
PDR 1 52.609
47.864 18.047 1.00 0.00<BR>HETATM 19 C19
PDR 1 52.323
45.695 16.799 1.00 0.00<BR>HETATM 20 H20
PDR 1 44.210
46.934 18.283 1.00 0.00<BR>HETATM 21 H21
PDR 1 42.045
47.532 19.182 1.00 0.00<BR>HETATM 22 H22
PDR 1 40.189
45.815 19.415 1.00 0.00<BR>HETATM 23 H23
PDR 1 40.502
43.512 18.747 1.00 0.00<BR>HETATM 24 H24
PDR 1 42.022
41.768 17.745 1.00 0.00<BR>HETATM 25 H25
PDR 1 44.262
41.102 16.703 1.00 0.00<BR>HETATM 26 H26
PDR 1 46.043
42.752 16.477 1.00 0.00<BR>HETATM 27 H27
PDR 1 46.604
45.386 19.200 1.00 0.00<BR>HETATM 28 H28
PDR 1 47.445
44.230 18.086 1.00 0.00<BR>HETATM 29 H29
PDR 1 48.112
46.449 16.767 1.00 0.00<BR>HETATM 30 H30
PDR 1 46.667
47.789 18.307 1.00 0.00<BR>HETATM 31 H31
PDR 1 49.482
46.012 19.479 1.00 0.00<BR>HETATM 32 H32
PDR 1 49.703
44.893 18.063 1.00 0.00<BR>HETATM 33 H33
PDR 1 50.059
47.894 17.760 1.00 0.00<BR>HETATM 34 H34
PDR 1 52.006
45.989 18.938 1.00 0.00<BR>HETATM 35 H35
PDR 1 52.229
48.461 18.906 1.00 0.00<BR>HETATM 36 H36
PDR 1 53.699
47.688 18.188 1.00 0.00<BR>HETATM 37 H37
PDR 1 52.451
48.451 17.115 1.00 0.00<BR>HETATM 38 H38
PDR 1 51.808
44.708 16.822 1.00 0.00<BR>HETATM 39 H39
PDR 1 52.067
46.197 15.838 1.00 0.00<BR>HETATM 40 H40
PDR 1 53.421
45.523 16.846 1.00 0.00<BR>CONECT
1 2 5
20
<BR>CONECT 2 3
21
<BR>CONECT 3 4
22
<BR>CONECT 4 6
23
<BR>CONECT 5 6
10
<BR>CONECT 6
7
<BR>CONECT 7 8
24
<BR>CONECT 8 9
25
<BR>CONECT 9 10
26
<BR>CONECT 10
11
<BR>CONECT 11
12
<BR>CONECT 12 13 27
28
<BR>CONECT 13 14 15
29
<BR>CONECT 14
30
<BR>CONECT 15 16 31
32
<BR>CONECT 16 17
33
<BR>CONECT 17 18 19
34
<BR>CONECT 18 35 36
37
<BR>CONECT 19 38 39
40
<BR>SPDBVT
1.0000000000
0.0000000000 0.0000000000
<BR>SPDBVT
0.0000000000
1.0000000000 0.0000000000
<BR>SPDBVT
0.0000000000
0.0000000000 1.0000000000
<BR>SPDBVT
0.0000000000
0.0000000000 0.0000000000
<BR>SPDBVT
0.0000000000
0.0000000000 0.0000000000
<BR>SPDBVV default;<BR>SPDBVV
45.752312478050
1769.439927720726
20.000000000000<BR>SPDBVV
0.8492806468
0.0177824961 0.5276420811
<BR>SPDBVV
0.4171748744
0.5899083148 -0.6913561342
<BR>SPDBVV
-0.3235544887
0.8072744038 0.4935793046
<BR>SPDBVV
46.9440002441
44.7815017700 17.6585006714
<BR>SPDBVV
0.0000000000
0.0000000000 0.0000000000
<BR>SPDBVf 23<BR>SPDBVl 1.00 1.00 1.00 <BR>SPDBVb 0.00 0.00
0.00<BR>END<BR></FONT></DIV>
<DIV><FONT face=Arial size=2>I have also tried the same file without numbers in
atom names and without connections.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><FONT face="Times New Roman" size=3>Any help will
be hightly appreciated.</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2><FONT face="Times New Roman"
size=3></FONT></FONT> </DIV>
<DIV><FONT face=Arial size=2><FONT face="Times New Roman" size=3>Sincerely
yours,</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2><FONT face="Times New Roman" size=3>V.
Tanchuk</FONT></DIV></FONT></BODY></HTML>