Dear users,<br>I have a problem related to PRODRG.<br><br>Chirality:NO <br>Full charges: YES<br>Energy minimization: NO<br>
<br><u><b>Ýnput file name:TRS.pdb</b></u><br>HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00 17.99 C <br>ANISOU 1803 C TRS B 232 2126 1948 2760 -378 45 -81 C <br>HETATM 1804 C1 TRS B 232 40.103 -5.057 65.899 1.00 16.81 C <br>
ANISOU 1804 C1 TRS B 232 1642 1577 3168 -531 171 120 C <br>HETATM 1805 C2 TRS B 232 37.795 -5.994 66.343 1.00 20.76 C <br>ANISOU 1805 C2 TRS B 232 2790 2021 3077 67 141 -408 C <br>
HETATM 1806 C3 TRS B 232 38.160 -3.717 67.031 1.00 16.86 C <br>ANISOU 1806 C3 TRS B 232 2240 1557 2611 -491 8 -192 C <br>HETATM 1807 N TRS B 232 38.227 -4.154 64.652 1.00 18.26 N <br>
ANISOU 1807 N TRS B 232 2336 2520 2083 -166 46 -112 N <br>HETATM 1808 O1 TRS B 232 40.741 -4.020 65.158 1.00 17.53 O <br>ANISOU 1808 O1 TRS B 232 1921 1579 3163 -225 147 197 O <br>
HETATM 1809 O2 TRS B 232 37.871 -6.803 65.211 1.00 23.91 O <br>ANISOU 1809 O2 TRS B 232 3018 2456 3610 -48 -86 -450 O <br>HETATM 1810 O3 TRS B 232 38.871 -2.531 66.874 1.00 18.28 O <br>
ANISOU 1810 O3 TRS B 232 2677 1594 2673 197 -4 -52 O <br><br>
I get the output <u>as the following file1.itp</u> from your PRODRG server for TRS ligand before 3-4 months. I think this calculate is correct:<br><b><u>file1.itp</u></b><br>................<br>[ moleculetype ]<br>; Name nrexcl<br>
TRS 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 OA 1 TRS O1 1 -0.240 15.9994 <br> 2 H 1 TRS HAA 1 0.052 1.0080 <br>
3 CH2 1 TRS C1 1 0.061 14.0270 <br> 4 CH1 1 TRS C 1 0.127 12.0110 <br> 5 CH2 1 TRS C3 2 0.090 14.0270 <br> 6 OA 1 TRS O3 2 -0.165 15.9994 <br>
7 H 1 TRS HAC 2 0.075 1.0080 <br> 8 NL 1 TRS N 3 0.876 14.0067 <br> 9 H 1 TRS HAE 3 0.041 1.0080 <br> 10 H 1 TRS HAF 3 0.042 1.0080 <br>
11 H 1 TRS HAD 3 0.041 1.0080 <br> 12 CH2 1 TRS C2 4 0.090 14.0270 <br> 13 OA 1 TRS O2 4 -0.165 15.9994 <br> 14 H 1 TRS HAB 4 0.075 1.0080 <br>
....................<br><br><br>
But Now, That is, today, I get the output <u>as the following file2.itp</u> from your PRODRG server for TRS ligand.<br><b><u>file2.itp</u></b><br>.....<br>[ moleculetype ]<br>; Name nrexcl<br>TRS 3<br><br>[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br> 1 OA 1 TRS O1 1 -0.173 15.9994 <br> 2 H 1 TRS H13 1 0.061 1.0080 <br> 3 CH2 1 TRS C1 1 0.165 14.0270 <br>
4 CCL4 1 TRS C 1 0.177 12.0110 <br> 5 CH2 1 TRS C3 1 0.165 14.0270 <br> 6 OA 1 TRS O3 1 -0.174 15.9994 <br> 7 H 1 TRS H33 1 0.062 1.0080 <br>
8 NL 1 TRS N 1 0.675 14.0067 <br> 9 H 1 TRS H2 1 0.014 1.0080 <br> 10 H 1 TRS H3 1 0.014 1.0080 <br> 11 H 1 TRS H1 1 0.014 1.0080 <br>
12 CH2 1 TRS C2 2 0.144 14.0270 <br> 13 OA 1 TRS O2 2 -0.198 15.9994 <br> 14 H 1 TRS H23 2 0.054 1.0080 <br>....<br><br>
Now, I think PRODRG calculate incorrectly cgnr charge<br clear="all"><br>
What should I do? can you help me?<br clear="all"><br>-- <br>Ahmet YILDIRIM<br>