Re: [gmx-users] about trifloroehanol
Thank you Justin .. I will follow your Instructions .. With Best Wishes, R.David -- gmx-users mailing listgmx-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
Re: [gmx-users] about trifloroehanol
Thank you justin.. I will try to adhere spacing -- gmx-users mailing listgmx-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
Re: [gmx-users] about trifloroehanol
On 5/15/12 8:25 AM, rama david wrote: Hi all Very sorry for my stupid question .. I really work a lot on these problem I wish to use Trifluroethanol as solvent for my study ... I Check the top file for G96 53a6 ff It shows TFE with following lines ... [ TFE ] [ atoms ] HT H 0.41000 0 OT OTFE-0.62500 0 CH2T CHTFE 0.27300 0 CT CTFE 0.45200 0 F1T FTFE-0.17000 0 F2T FTFE-0.17000 0 F3T FTFE-0.17000 0 [ bonds ] HTOTgb_1 OT CH2Tgb_18 CH2TCTgb_27 CT F1Tgb_13 CT F2Tgb_13 CT F3Tgb_13 [ angles ] ; aiajak gromos type HTOT CH2T ga_50 OT CH2TCT ga_51 CH2TCT F1T ga_52 CH2TCT F2T ga_52 CH2TCT F3T ga_52 F1TCT F2T ga_49 F1TCT F3T ga_49 F2TCT F3T ga_49 [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type HTOT CH2TCT gd_24 I draw TFE with Avogadro software... I get following pdb .. COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 C LIG 1 -7.301 3.857 0.070 1.00 0.00 C HETATM2 C LIG 1 -6.798 2.416 0.102 1.00 0.00 C HETATM3 F LIG 1 -8.626 3.915 0.327 1.00 0.00 F HETATM4 F LIG 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM5 F LIG 1 -6.668 4.631 0.977 1.00 0.00 F HETATM6 O LIG 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM7 H LIG 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM8 H LIG 1 -6.898 2.006 1.111 1.00 0.00 H HETATM9 H LIG 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT12345 CONECT1 CONECT21678 CONECT2 CONECT31 CONECT41 CONECT51 CONECT629 CONECT72 CONECT82 CONECT96 MASTER000000009090 END I change pdb as follow to match the nomenclature with G96 53a6 ff (Is it right or wrong ) OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 CT TFE 1 -7.301 3.857 0.070 1.00 0.00 C HETATM2 CH2T TFE 1 -6.798 2.416 0.102 1.00 0.00 C HETATM3 F1T TFE 1 -8.626 3.915 0.327 1.00 0.00 F HETATM4 F2T TFE 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM5 F3T TFE 1 -6.668 4.631 0.977 1.00 0.00 F HETATM6 OT TFE 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM7H TFE 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM8H TFE 1 -6.898 2.006 1.111 1.00 0.00 H HETATM9 HT TFE 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT12345 AFTER running pdb2gmx -ignh I got following error -- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue 'F' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I tried a lot ... Please give me some suggestion ... Thank you in Advance ... The column spacing of a .pdb file is fixed and you must adhere to it. The changes you have made look fine, but they are spaced incorrectly, thus pdb2gmx is not able to correctly read its contents. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
[gmx-users] about trifloroehanol
Hi all Very sorry for my stupid question .. I really work a lot on these problem I wish to use Trifluroethanol as solvent for my study ... I Check the top file for G96 53a6 ff It shows TFE with following lines ... [ TFE ] [ atoms ] HT H 0.41000 0 OT OTFE-0.62500 0 CH2T CHTFE 0.27300 0 CT CTFE 0.45200 0 F1T FTFE-0.17000 0 F2T FTFE-0.17000 0 F3T FTFE-0.17000 0 [ bonds ] HTOTgb_1 OT CH2Tgb_18 CH2TCTgb_27 CT F1Tgb_13 CT F2Tgb_13 CT F3Tgb_13 [ angles ] ; aiajak gromos type HTOT CH2T ga_50 OT CH2TCT ga_51 CH2TCT F1T ga_52 CH2TCT F2T ga_52 CH2TCT F3T ga_52 F1TCT F2T ga_49 F1TCT F3T ga_49 F2TCT F3T ga_49 [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type HTOT CH2TCT gd_24 I draw TFE with Avogadro software... I get following pdb .. COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 C LIG 1 -7.301 3.857 0.070 1.00 0.00 C HETATM2 C LIG 1 -6.798 2.416 0.102 1.00 0.00 C HETATM3 F LIG 1 -8.626 3.915 0.327 1.00 0.00 F HETATM4 F LIG 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM5 F LIG 1 -6.668 4.631 0.977 1.00 0.00 F HETATM6 O LIG 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM7 H LIG 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM8 H LIG 1 -6.898 2.006 1.111 1.00 0.00 H HETATM9 H LIG 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT12345 CONECT1 CONECT21678 CONECT2 CONECT31 CONECT41 CONECT51 CONECT629 CONECT72 CONECT82 CONECT96 MASTER000000009090 END I change pdb as follow to match the nomenclature with G96 53a6 ff (Is it right or wrong ) OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 CT TFE 1 -7.301 3.857 0.070 1.00 0.00 C HETATM2 CH2T TFE 1 -6.798 2.416 0.102 1.00 0.00 C HETATM3 F1T TFE 1 -8.626 3.915 0.327 1.00 0.00 F HETATM4 F2T TFE 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM5 F3T TFE 1 -6.668 4.631 0.977 1.00 0.00 F HETATM6 OT TFE 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM7H TFE 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM8H TFE 1 -6.898 2.006 1.111 1.00 0.00 H HETATM9 HT TFE 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT12345 AFTER running pdb2gmx -ignh I got following error -- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue 'F' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I tried a lot ... Please give me some suggestion ... Thank you in Advance ... Rama David ... -- gmx-users mailing listgmx-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
Re: [gmx-users] about trifloroehanol
On 5/15/12 9:54 AM, rama david wrote: Hi to all Sorry Justin , I try to correct spacing but now it stuck to another problem pdb to TFE is as follow OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 ATOM 1 CT TFE 1 -5.510 2.534 0.093 1.00 0.00 C ATOM 2 CH2T TFE 1 -6.061 1.111 0.155 1.00 0.00 C ATOM 3 F1T TFE 1 -5.017 2.899 1.300 1.00 0.00 F ATOM 4 F2T TFE 1 -6.461 3.426 -0.251 1.00 0.00 F ATOM 5 F3T TFE 1 -4.506 2.627 -0.806 1.00 0.00 F ATOM 6 OT TFE 1 -7.065 0.921 1.164 1.00 0.00 O ATOM 7H TFE 1 -5.248 0.409 0.367 1.00 0.00 H ATOM 8H TFE 1 -6.500 0.837 -0.808 1.00 0.00 H ATOM 9 HT TFE 1 -6.742 1.339 1.982 1.00 0.00 H The spacing in this file is still potentially problematic. CONECT12345 CONECT1 CONECT21678 CONECT2 CONECT31 CONECT41 CONECT51 CONECT629 CONECT72 CONECT82 CONECT96 MASTER000000009090 END after giving pdb2gmx -ignh If you delete the two extraneous H atoms in the .pdb file and omit -ignh, you won't have this problem. It give following error WARNING: atom HT is missing in residue TFE 1 in the pdb file You might need to add atom HT to the hydrogen database of building block TFE in the file aminoacids.hdb (see the manual) --- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1463 Fatal error: There were 1 missing atoms in molecule Other, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- --- now I know go with missing is wrong ..But to check error I goes with -missing flag . the output confo.gro is as follow UNNAMED 6 1TFE OT1 -0.706 0.092 0.116 1TFE CH2T2 -0.606 0.111 0.015 1TFE CT3 -0.551 0.253 0.009 1TFEF1T4 -0.502 0.290 0.130 1TFEF2T5 -0.646 0.343 -0.025 1TFEF3T6 -0.451 0.263 -0.081 0.25590 0.25050 0.21060 The hydrogen attched to oxyge is missing .. The entry to these hydrogen as HT is mentioned in pdb file ... The warning message is self-explanatory. I will be a very greatfull to you if you told me how to add HT in aminoacids.hdb Aminoacids.hdb file is as follow SER 2 11HN-CCA 12HGOGCBCA *TFE 1 12HOCH2C* The corrected line would read: 12HTOTCH2TCT This is a small bug that should probably be fixed, though in your case, with proper input, use of the .hdb file is unnecessary. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] about trifloroehanol
Hi to all Sorry Justin , I try to correct spacing but now it stuck to another problem pdb to TFE is as follow OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 ATOM 1 CT TFE 1 -5.510 2.534 0.093 1.00 0.00 C ATOM 2 CH2T TFE 1 -6.061 1.111 0.155 1.00 0.00 C ATOM 3 F1T TFE 1 -5.017 2.899 1.300 1.00 0.00 F ATOM 4 F2T TFE 1 -6.461 3.426 -0.251 1.00 0.00 F ATOM 5 F3T TFE 1 -4.506 2.627 -0.806 1.00 0.00 F ATOM 6 OT TFE 1 -7.065 0.921 1.164 1.00 0.00 O ATOM 7H TFE 1 -5.248 0.409 0.367 1.00 0.00 H ATOM 8H TFE 1 -6.500 0.837 -0.808 1.00 0.00 H ATOM 9 HT TFE 1 -6.742 1.339 1.982 1.00 0.00 H CONECT12345 CONECT1 CONECT21678 CONECT2 CONECT31 CONECT41 CONECT51 CONECT629 CONECT72 CONECT82 CONECT96 MASTER000000009090 END after giving pdb2gmx -ignh It give following error WARNING: atom HT is missing in residue TFE 1 in the pdb file You might need to add atom HT to the hydrogen database of building block TFE in the file aminoacids.hdb (see the manual) --- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1463 Fatal error: There were 1 missing atoms in molecule Other, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- --- now I know go with missing is wrong ..But to check error I goes with -missing flag . the output confo.gro is as follow UNNAMED 6 1TFE OT1 -0.706 0.092 0.116 1TFE CH2T2 -0.606 0.111 0.015 1TFE CT3 -0.551 0.253 0.009 1TFEF1T4 -0.502 0.290 0.130 1TFEF2T5 -0.646 0.343 -0.025 1TFEF3T6 -0.451 0.263 -0.081 0.25590 0.25050 0.21060 The hydrogen attched to oxyge is missing .. The entry to these hydrogen as HT is mentioned in pdb file ... The warning message is self-explanatory. I will be a very greatfull to you if you told me how to add HT in aminoacids.hdb Aminoacids.hdb file is as follow SER 2 11HN-CCA 12HGOGCBCA *TFE 1 12HOCH2C* THR 2 11HN-CCA 12HG1OG1CBCA TRP 7 11HN-CCA 11HD1CD1CGNE1 So What line I have to add here??? Please suggest me the way out to get rid from error .. Rama David -- gmx-users mailing listgmx-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
