Hi Ahmet, The PRODRG server is not related to Gromacs. If you encounter problems pertaining to the server or the outcome from it, you should drop a line to the PRODRG development team.
Cheers, Tsjerk 2011/9/17 ahmet yıldırım <ahmedo...@gmail.com>: > 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 > > What should I do? can you help me? > > -- > Ahmet YILDIRIM > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands
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