Dear Tsjerk and Justin, Thanks for your reply. I will contact the PRODRG developers. can you suggest anyway/anytool for generating ligand coordinates/topologies?
Thanks in advance 17 Eylül 2011 15:58 tarihinde Justin A. Lemkul <[email protected]> yazdı: > > > ahmet yıldırım wrote: > >> Dear users, >> I have a problem related to PRODRG. >> >> Chirality:NO >> Full charges: YES >> Energy minimization: NO >> >> _*İnput file name:TRS.pdb*_ >> 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 >> >> 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: >> *_file1.itp_* >> ................ >> [ moleculetype ] >> ; Name nrexcl >> TRS 3 >> >> [ atoms ] >> ; nr type resnr resid atom cgnr charge mass >> 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 .................... >> >> >> But Now, That is, today, I get the output _as the following file2.itp_ >> from your PRODRG server for TRS ligand. >> *_file2.itp_* >> ..... >> [ moleculetype ] >> ; Name nrexcl >> TRS 3 >> >> [ atoms ] >> ; nr type resnr resid atom cgnr charge mass >> 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 .... >> >> Now, I think PRODRG calculate incorrectly cgnr charge >> >> > 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): > > http://pubs.acs.org/doi/abs/**10.1021/ci100335w<http://pubs.acs.org/doi/abs/10.1021/ci100335w> > > -Justin > > > What should I do? can you help me? >> >> -- >> Ahmet YILDIRIM >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM
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