Dear Tsjerk and Justin,<br>
<br>
Thanks for your reply. I will contact the PRODRG developers. <br>can you suggest anyway/anytool for generating ligand coordinates/topologies? <br><br>Thanks in advance<br><br><div class="gmail_quote">17 Eylül 2011 15:58 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdı:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear users,<br>
I have a problem related to PRODRG.<br>
<br>
Chirality:NO<br>
Full charges: YES<br>
Energy minimization: NO<br>
<br>
_*İnput file name:TRS.pdb*_<br>
HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00 17.99 C ANISOU 1803 C TRS B 232 2126 1948 2760 -378 45 -81 C HETATM 1804 C1 TRS B 232 40.103 -5.057 65.899 1.00 16.81 C ANISOU 1804 C1 TRS B 232 1642 1577 3168 -531 171 120 C HETATM 1805 C2 TRS B 232 37.795 -5.994 66.343 1.00 20.76 C ANISOU 1805 C2 TRS B 232 2790 2021 3077 67 141 -408 C HETATM 1806 C3 TRS B 232 38.160 -3.717 67.031 1.00 16.86 C ANISOU 1806 C3 TRS B 232 2240 1557 2611 -491 8 -192 C HETATM 1807 N TRS B 232 38.227 -4.154 64.652 1.00 18.26 N ANISOU 1807 N TRS B 232 2336 2520 2083 -166 46 -112 N HETATM 1808 O1 TRS B 232 40.741 -4.020 65.158 1.00 17.53 O ANISOU 1808 O1 TRS B 232 1921 1579 3163 -225 147 197 O HETATM 1809 O2 TRS B 232 37.871 -6.803 65.211 1.00 23.91 O ANISOU 1809 O2 TRS B 232 3018 2456 3610 -48 -86 -450 O HETATM 1810 O3 TRS B 232 38.871 -2.531 66.874 1.00 18.28 O ANISOU 1810 O3 TRS B 232 2677 1594 2673 197 -4 -52 O<br>
<br>
I get the output _as the following file1.itp_ from your PRODRG server for TRS ligand before 3-4 months. I think this calculate is correct:<br>
*_file1.itp_*<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 2 H 1 TRS HAA 1 0.052 1.0080 3 CH2 1 TRS C1 1 0.061 14.0270 4 CH1 1 TRS C 1 0.127 12.0110 5 CH2 1 TRS C3 2 0.090 14.0270 6 OA 1 TRS O3 2 -0.165 15.9994 7 H 1 TRS HAC 2 0.075 1.0080 8 NL 1 TRS N 3 0.876 14.0067 9 H 1 TRS HAE 3 0.041 1.0080 10 H 1 TRS HAF 3 0.042 1.0080 11 H 1 TRS HAD 3 0.041 1.0080 12 CH2 1 TRS C2 4 0.090 14.0270 13 OA 1 TRS O2 4 -0.165 15.9994 14 H 1 TRS HAB 4 0.075 1.0080 ....................<br>
<br>
<br>
But Now, That is, today, I get the output _as the following file2.itp_ from your PRODRG server for TRS ligand.<br>
*_file2.itp_*<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 2 H 1 TRS H13 1 0.061 1.0080 3 CH2 1 TRS C1 1 0.165 14.0270 4 CCL4 1 TRS C 1 0.177 12.0110 5 CH2 1 TRS C3 1 0.165 14.0270 6 OA 1 TRS O3 1 -0.174 15.9994 7 H 1 TRS H33 1 0.062 1.0080 8 NL 1 TRS N 1 0.675 14.0067 9 H 1 TRS H2 1 0.014 1.0080 10 H 1 TRS H3 1 0.014 1.0080 11 H 1 TRS H1 1 0.014 1.0080 12 CH2 1 TRS C2 2 0.144 14.0270 13 OA 1 TRS O2 2 -0.198 15.9994 14 H 1 TRS H23 2 0.054 1.0080 ....<br>
<br>
Now, I think PRODRG calculate incorrectly cgnr charge<br>
<br>
</blockquote>
<br></div></div>
I agree with Tsjerk that you should contact the PRODRG developers regarding the differences, but I would also say that neither of these files is correct. PRODRG has never given reliable charges. See, for instance (something I posted dozens of times before):<br>
<br>
<a href="http://pubs.acs.org/doi/abs/10.1021/ci100335w" target="_blank">http://pubs.acs.org/doi/abs/<u></u>10.1021/ci100335w</a><br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
What should I do? can you help me?<br>
<br>
-- <br>
Ahmet YILDIRIM<br>
<br>
</blockquote>
<br></div>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
-- <br></font><div><div></div><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>