Re: [gmx-users] add a group to an amino acid
Thank you very much, Mark! The problem was for the type CG2 in .rtp. I corrected it and the errors disappear.[?] (I should study more for that non-zero charge, i think.) 332.gif-- 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] add a group to an amino acid
On 16/11/2010 9:04 PM, hengame fallah wrote: Thank you very much, Mark! Now i have errors from my .top file after grompp command. The question is that why in pdb2gmx, editconf ,genbox and make_ndx steps i don't see these errors: ... processing topology... Opening library file /usr/share/gromacs/top/ffoplsaa.itp Opening library file /usr/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations ERROR 1 [file topol.top, line 412]: No default Angle types ERROR 2 [file topol.top, line 567]: No default Ryckaert-Bell. types ERROR 3 [file topol.top, line 570]: No default Ryckaert-Bell. types ERROR 4 [file topol.top, line 573]: No default Ryckaert-Bell. types ERROR 5 [file topol.top, line 580]: No default Ryckaert-Bell. types ERROR 6 [file topol.top, line 581]: No default Ryckaert-Bell. types ERROR 7 [file topol.top, line 582]: No default Ryckaert-Bell. types Opening library file /usr/share/gromacs/top/spc.itp Opening library file /usr/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 664]: System has non-zero total charge: 6.00e-02 0.06 means your residue's charges do not add to zero, and they should. processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/grompp.c, line: 986 Fatal error: There were 7 errors in input file(s) *topol.top:* ... 43 opls_238 3BOC N 17 -0.514.0067 ; qtot 0.5 44 opls_241 3BOC H 170.3 1.008 ; qtot 0.8 45 opls_283 3BOC CA 17 0.04 12.011 ; qtot 0.84 46 opls_140 3BOC HA1 17 0.06 1.008 ; qtot 0.9 47 opls_140 3BOC HA2 17 0.06 1.008 ; qtot 0.96 48 opls_149 3BOC CB 18 0.055 12.011 ; qtot 1.015 49 opls_140 3BOC HB 18 0.06 1.008 ; qtot 1.075 50 opls_145 3BOCCG1 18 -0.115 12.011 ; qtot 0.96 51 opls_145 3BOCCD1 19 -0.115 12.011 ; qtot 0.845 52 opls_146 3BOCHD1 19 0.115 1.008 ; qtot 0.96 53 opls_145 3BOCCD2 20 -0.115 12.011 ; qtot 0.845 54 opls_146 3BOCHD2 20 0.115 1.008 ; qtot 0.96 55 opls_145 3BOCCE1 21 -0.115 12.011 ; qtot 0.845 56 opls_146 3BOCHE1 21 0.115 1.008 ; qtot 0.96 57 opls_145 3BOCCE2 22 -0.115 12.011 ; qtot 0.845 58 opls_146 3BOCHE2 22 0.115 1.008 ; qtot 0.96 59 opls_145 3BOC CZ 23 1 12.011 ; qtot 1.96 60 opls_264 3BOC Cl23 -1 35.453 ; qtot 0.96 61 opls_224B 3BOC CG2 24 -0.12 12.011 ; qtot 0.84 62 opls_140 3BOC HG1 24 0.06 1.008 ; qtot 0.9 63 opls_140 3BOC HG2 24 0.06 1.008 ; qtot 0.96 64 opls_271 3BOC C 250.7 12.011 ; qtot 1.66 65 opls_272 3BOC O1 25 -0.815.9994 ; qtot 0.86 66 opls_272 3BOC O2 25 -0.815.9994 ; qtot 0.06 ... [ angles ] ... line 412: 454861 1 ... [ dihedrals ] ... line 567: 43454861 3 ... line 570: 46454861 3 ... line 573: 47454861 3 ... line 580: 45486162 3 line 581: 45486163 3 line 582: 45486164 3 ... it seems that 45 4861 is the problem. CACBCG2 Where i should define angle type for it? Those three atoms have types. The type of function to put on an angle whose three atoms have given types is defined in the force field. Evidently, there isn't one for the types of these atoms. This relates to choosing your atom types properly, like I've said twice before now. Go and look up their types in the .rtp, and then look up in the .atp what environments the types for which they were parameterized, and see what your non sequitur is. Mark -- 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
Re: [gmx-users] add a group to an amino acid
Dear Mark, I think that i couldn't explain my problem clearly, however i have changed my .rtp but i don't know how should be my .hdb file. a) The structure of *BOC* is: *-CO-CH2-CH(C6H5Cl)-CH2-NH-* b) This is the new charges: [ BOC ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.080 1 HA1opls_1400.060 1 HA2opls_1400.060 1 CBopls_1490.055 2 HBopls_1400.060 2 CG1opls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_1451.000 7 Clopls_264 -1.000 7 CG2opls_071 -0.120 8 HG1opls_1400.060 8 HG2opls_1400.060 8 Copls_2350.700 9 Oopls_236 -0.700 9 c) charge for CG1 in PHE (in OPLS .rtp) is negative, too. d) Would you explain for me that what is wrong in my atom types? e) As you see in the error, at first there are 63 residues (like my pdb) but when when it adds COO- and NH3+ there are 69 residues! it should add only one O (for COO-) and two Hs for (NH3+) i think. There are 1 chains and 0 blocks of water and 3 residues with 63 atoms chain #res #atoms 1 ' ' 3 63 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Residue 57 Sorting it all out... Opening library file /usr/share/gromacs/top/ffoplsaa.hdb Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.3# Processing chain 1 (63 atoms, 3 residues) There are 3 donors and 3 acceptors There are 4 hydrogen bonds Checking for duplicate atoms Opening library file /usr/share/gromacs/top/specbond.dat 7 out of 7 lines of specbond.dat converted succesfully N-terminus: NH3+ C-terminus: COO- Now there are 3 residues with 69 atoms Making bonds... Warning: Long Bond (53-54 = 0.334847 nm) Warning: Long Bond (53-56 = 0.334912 nm) Warning: Long Bond (64-65 = 0.271173 nm) Warning: Long Bond (64-66 = 0.347808 nm) Warning: Long Bond (64-67 = 0.31288 nm) Opening library file /usr/share/gromacs/top/aminoacids.dat --- Program pdb2gmx, VERSION 4.0.7 Source code file: ../../../../src/kernel/add_par.c, line: 233 Fatal error: Atom HB1 not found in rtp database in residue BOC, it looks a bit like HB -- 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] add a group to an amino acid
On 14/11/2010 7:26 PM, hengame fallah wrote: Dear Mark, I think that i couldn't explain my problem clearly, however i have changed my .rtp but i don't know how should be my .hdb file. a) The structure of *_BOC_* is: *-CO-CH2-CH(C6H5Cl)-CH2-NH-* Great. b) This is the new charges: [ BOC ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.080 1 HA1opls_1400.060 1 HA2opls_1400.060 1 CBopls_1490.055 2 HBopls_1400.060 2 CG1opls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_1451.000 7 Clopls_264 -1.000 7 CG2opls_071 -0.120 8 HG1opls_1400.060 8 HG2opls_1400.060 8 Copls_2350.700 9 Oopls_236 -0.700 9 This looks much better. c) charge for CG1 in PHE (in OPLS .rtp) is negative, too. OK d) Would you explain for me that what is wrong in my atom types? No. My point last email was that you may need to consider what atom types are suitable for your backbone methylene C. I don't know what is suitable. You will have to look at the .atp file and perhaps read OPLS/AA papers. e) As you see in the error, at first there are 63 residues (like my pdb) but when when it adds COO- and NH3+ there are 69 residues! it should add only one O (for COO-) and two Hs for (NH3+) i think. Well, what do the .tdb files say? You should model these for BOC upon the PHE ones, of course. You will need to have read the parts of chapter 5 that pertain to the .hdb and .tdb files. There are 1 chains and 0 blocks of water and 3 residues with 63 atoms chain #res #atoms 1 ' ' 3 63 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Residue 57 Sorting it all out... Opening library file /usr/share/gromacs/top/ffoplsaa.hdb Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.3# Processing chain 1 (63 atoms, 3 residues) There are 3 donors and 3 acceptors There are 4 hydrogen bonds Checking for duplicate atoms Opening library file /usr/share/gromacs/top/specbond.dat 7 out of 7 lines of specbond.dat converted succesfully N-terminus: NH3+ C-terminus: COO- Now there are 3 residues with 69 atoms Making bonds... Warning: Long Bond (53-54 = 0.334847 nm) Warning: Long Bond (53-56 = 0.334912 nm) Warning: Long Bond (64-65 = 0.271173 nm) Warning: Long Bond (64-66 = 0.347808 nm) Warning: Long Bond (64-67 = 0.31288 nm) These warnings are still suggestive that your atom coordinates are labelled inappropriately in your coordinate file. Opening library file /usr/share/gromacs/top/aminoacids.dat --- Program pdb2gmx, VERSION 4.0.7 Source code file: ../../../../src/kernel/add_par.c, line: 233 Fatal error: Atom HB1 not found in rtp database in residue BOC, it looks a bit like HB I think your .hdb is still trying to add two hydrogens to CB. Mark -- 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] add a group to an amino acid
I read about .hdb file and then i editted my .hdb file: ... BOC 9 11H N -CCA 26HA CA N CB 15HB CB CA CG1CG2 11HD1CD1CG1CE1 11HD2CD2CG1CE2 11HE1CE1CD1CZ 11HE2CE2CD2CZ 26HG CG2CB C CYS23 11H N-C CA 15HACAN CCB 26HBCBSGCA ... PHE 8 11H N -C CA 15HA CA N CCB 26HB CB CGCA 11HD1CD1CGCE1 11HD2CD2CGCE2 11HE1CE1CD1CZ 11HE2CE2CD2CZ 11HZ CZ CE1CE2 ... but i got this error: ... There are 1 chains and 0 blocks of water and 3 residues with 63 atoms chain #res #atoms 1 ' ' 3 63 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Residue 57 Sorting it all out... Opening library file /usr/share/gromacs/top/ffoplsaa.hdb --- Program pdb2gmx, VERSION 4.0.7 Source code file: ../../../../src/kernel/h_db.c, line: 87 Fatal error: wrong format in input file ffoplsaa.hdb on line CYS23 -- 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] add a group to an amino acid
On 14/11/2010 8:13 PM, hengame fallah wrote: I read about .hdb file and then i editted my .hdb file: ... BOC 9 Then you'll know from your reading what this number should be :-) It's the number of types of hydrogen atoms that might be added. For each of them, there's one line below. You needed to have left this on 8. Because you've changed it to 9, pdb2gmx tries to make sense of a ninth line, which is CYS2 3 and gives you the error you saw. Mark 11H N -CCA 26HA CA N CB 15HB CB CA CG1CG2 11HD1CD1CG1CE1 11HD2CD2CG1CE2 11HE1CE1CD1CZ 11HE2CE2CD2CZ 26HG CG2CB C CYS23 11H N-C CA 15HACAN CCB 26HBCBSGCA ... PHE 8 11H N -C CA 15HA CA N CCB 26HB CB CGCA 11HD1CD1CGCE1 11HD2CD2CGCE2 11HE1CE1CD1CZ 11HE2CE2CD2CZ 11HZ CZ CE1CE2 ... but i got this error: ... There are 1 chains and 0 blocks of water and 3 residues with 63 atoms chain #res #atoms 1 ' ' 3 63 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Residue 57 Sorting it all out... Opening library file /usr/share/gromacs/top/ffoplsaa.hdb --- Program pdb2gmx, VERSION 4.0.7 Source code file: ../../../../src/kernel/h_db.c, line: 87 Fatal error: wrong format in input file ffoplsaa.hdb on line CYS23 -- 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] add a group to an amino acid
Thanks Justin, actually the protein that i want to simulate consists of two amino acids: PHE and BOC BOC is an unusual amino acid as you know. It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE I finally defined a residue BOC in opls .rtp file: [ BOC ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B -0.005 1 HA1opls_1400.060 1 HA2opls_1400.060 1 CBopls_1490.140 2 HB1opls_1400.060 2 CG1opls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_1450.885 7 Clopls_264 -1.000 7 CG2opls_071 -0.005 8 HG1opls_1400.060 8 HG2opls_1400.060 8 Copls_2350.700 9 Oopls_236 -0.700 9 the ending part of my PDB is: ... ATOM 38 HE2 PHE 2 -6.946 8.455 4.409 ATOM 39 CZ PHE 2 -5.456 10.015 4.624 ATOM 40 HZ PHE 2 -5.887 10.646 3.828 ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540 6.235 4.026 ATOM 45 CB BOC 3 -1.797 4.794 2.924 ATOM 46 HB1 BOC 3 -2.244 3.809 3.204 ATOM 47 CG1 BOC 3 -2.976 5.730 2.589 ATOM 48 CG2 BOC 3 -0.935 4.544 1.698 ATOM 49 CD1 BOC 3 -1.231 3.466 0.845 ATOM 50 HD1 BOC 3 -2.070 2.790 1.081 ATOM 51 CD2 BOC 3 0.120 5.408 1.353 ATOM 52 HD2 BOC 3 0.357 6.277 1.986 ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312 ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964 ATOM 55 CE2 BOC 3 0.881 5.182 0.197 ATOM 56 HE2 BOC 3 1.706 5.870 -0.054 ATOM 57 CZ BOC 3 0.591 4.093 -0.639 ATOM 58 C BOC 3 -2.565 7.148 2.291 ATOM 59 O BOC 3 -2.716 8.035 3.131 ATOM 60 CL BOC 3 1.525 3.816 -2.062 ATOM 61 HA2 BOC 3 -0.172 4.511 4.360 ATOM 62 HG1 BOC 3 -3.530 5.331 1.707 ATOM 63 HG2 BOC 3 -3.708 5.729 3.431 Now i got t this error: ... There are 1 chains and 0 blocks of water and 3 residues with 63 atoms chain #res #atoms 1 ' ' 3 63 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Residue 57 Sorting it all out... Opening library file /usr/share/gromacs/top/ffoplsaa.hdb Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.69# Processing chain 1 (63 atoms, 3 residues) There are 3 donors and 3 acceptors There are 4 hydrogen bonds Checking for duplicate atoms Opening library file /usr/share/gromacs/top/specbond.dat 7 out of 7 lines of specbond.dat converted succesfully N-terminus: NH3+ C-terminus: COO- Now there are 3 residues with 68 atoms Making bonds... Warning: Long Bond (52-53 = 0.334847 nm) Warning: Long Bond (52-55 = 0.334912 nm) Warning: Long Bond (63-64 = 0.271173 nm) Warning: Long Bond (63-65 = 0.347808 nm) Warning: Long Bond (63-66 = 0.31288 nm) Opening library file /usr/share/gromacs/top/aminoacids.dat --- Program pdb2gmx, VERSION 4.0.7 Source code file: ../../../../src/kernel/add_par.c, line: 233 Fatal error: Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1 --- ... What should i do? On Sun, Nov 7, 2010 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: hengame fallah wrote: Hi, I'm using the OPLS force field. [ PHE ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_145 -0.115 7 HZopls_1460.115 7 Copls_2350.500 8 Oopls_236 -0.500 8 I want to attach CL atom instead of HZ i made my pdb but
Re: [gmx-users] add a group to an amino acid
On 9/11/2010 8:19 PM, hengame fallah wrote: Thanks Justin, actually the protein that i want to simulate consists of two amino acids: PHE and BOC BOC is an unusual amino acid as you know. It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE So that probably means you'll have to pay care to the [bonds] section in the .rtp file. The only bonds GROMACS knows about are the ones in the .rtp. They have to be right. The errors below look like you haven't done it right. I finally defined a residue BOC in opls .rtp file: [ BOC ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B -0.005 1 HA1opls_1400.060 1 HA2opls_1400.060 1 CBopls_1490.140 2 HB1opls_1400.060 2 CG1opls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_1450.885 7 Clopls_264 -1.000 7 CG2opls_071 -0.005 8 HG1opls_1400.060 8 HG2opls_1400.060 8 Copls_2350.700 9 Oopls_236 -0.700 9 the ending part of my PDB is: ... ATOM 38 HE2 PHE 2 -6.946 8.455 4.409 ATOM 39 CZ PHE 2 -5.456 10.015 4.624 ATOM 40 HZ PHE 2 -5.887 10.646 3.828 ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540 6.235 4.026 HA2 is missing here, per your .rtp ATOM 45 CB BOC 3 -1.797 4.794 2.924 ATOM 46 HB1 BOC 3 -2.244 3.809 3.204 ATOM 47 CG1 BOC 3 -2.976 5.730 2.589 ATOM 48 CG2 BOC 3 -0.935 4.544 1.698 ATOM 49 CD1 BOC 3 -1.231 3.466 0.845 ATOM 50 HD1 BOC 3 -2.070 2.790 1.081 ATOM 51 CD2 BOC 3 0.120 5.408 1.353 ATOM 52 HD2 BOC 3 0.357 6.277 1.986 ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312 ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964 ATOM 55 CE2 BOC 3 0.881 5.182 0.197 ATOM 56 HE2 BOC 3 1.706 5.870 -0.054 ATOM 57 CZ BOC 3 0.591 4.093 -0.639 ATOM 58 C BOC 3 -2.565 7.148 2.291 ATOM 59 O BOC 3 -2.716 8.035 3.131 ATOM 60 CL BOC 3 1.525 3.816 -2.062 ATOM 61 HA2 BOC 3 -0.172 4.511 4.360 ATOM 62 HG1 BOC 3 -3.530 5.331 1.707 ATOM 63 HG2 BOC 3 -3.708 5.729 3.431 Now i got t this error: ... There are 1 chains and 0 blocks of water and 3 residues with 63 atoms chain #res #atoms 1 ' ' 3 63 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Residue 57 Sorting it all out... Opening library file /usr/share/gromacs/top/ffoplsaa.hdb Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.69# Processing chain 1 (63 atoms, 3 residues) There are 3 donors and 3 acceptors There are 4 hydrogen bonds Checking for duplicate atoms Opening library file /usr/share/gromacs/top/specbond.dat 7 out of 7 lines of specbond.dat converted succesfully N-terminus: NH3+ C-terminus: COO- Now there are 3 residues with 68 atoms Making bonds... Warning: Long Bond (52-53 = 0.334847 nm) Warning: Long Bond (52-55 = 0.334912 nm) Warning: Long Bond (63-64 = 0.271173 nm) Warning: Long Bond (63-65 = 0.347808 nm) Warning: Long Bond (63-66 = 0.31288 nm) This is telling you the connectivity in your .rtp doesn't match the spatial arrangement very well. Go back and check the .rtp file. Opening library file /usr/share/gromacs/top/aminoacids.dat --- Program pdb2gmx, VERSION 4.0.7 Source code file: ../../../../src/kernel/add_par.c, line: 233 Fatal error: Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1 pdb2gmx is probably hopelessly confused by now. Fix the other issues and try again. Mark --- ... What should i do? On Sun, Nov 7, 2010 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: hengame fallah wrote: Hi, I'm using the OPLS force field. [ PHE ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1
Re: [gmx-users] add a group to an amino acid
Dear Mark, I edited my pdb like this: ... ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540 6.235 4.026 ATOM 45 HA2 BOC 3 -0.172 4.511 4.360 ATOM 46 CB BOC 3 -1.797 4.794 2.924 ATOM 47 HB1 BOC 3 -2.244 3.809 3.204 ATOM 48 CG1 BOC 3 -2.976 5.730 2.589 ATOM 49 CD1 BOC 3 -1.231 3.466 0.845 ATOM 50 HD1 BOC 3 -2.070 2.790 1.081 ATOM 51 CD2 BOC 3 0.120 5.408 1.353 ATOM 52 HD2 BOC 3 0.357 6.277 1.986 ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312 ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964 ATOM 55 CE2 BOC 3 0.881 5.182 0.197 ATOM 56 HE2 BOC 3 1.706 5.870 -0.054 ATOM 57 CZ BOC 3 0.591 4.093 -0.639 ATOM 58 CG2 BOC 3 -0.935 4.544 1.698 ATOM 59 HG1 BOC 3 -3.530 5.331 1.707 ATOM 60 HG2 BOC 3 -3.708 5.729 3.431 ATOM 61 C BOC 3 -2.565 7.148 2.291 ATOM 62 O BOC 3 -2.716 8.035 3.131 ATOM 63 Cl BOC 3 1.525 3.816 -2.062 END and my .rtp file for [ BOC ] is: [ BOC ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B -0.005 1 HA1opls_1400.060 1 HA2opls_1400.060 1 CBopls_1490.140 2 HB1opls_1400.060 2 CG1opls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_1450.885 7 Clopls_264 -1.000 7 CG2opls_071 -0.005 8 HG1opls_1400.060 8 HG2opls_1400.060 8 Copls_2350.700 9 Oopls_236 -0.700 9 [ bonds ] N H NCA CA HA1 CA HA2 CACB CB HB1 CB CG1 CB CG2 CG1 CD1 CG1 CD2 CD1 HD1 CD1 CE1 CD2 HD2 CD2 CE2 CE1 HE1 CE1CZ CE2 HE2 CE2CZ CZCl CG2 HG1 CG2 HG2 CG2 C C O -C N and still i got that error! Fatal error: Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1 On Tue, Nov 9, 2010 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/11/2010 8:19 PM, hengame fallah wrote: Thanks Justin, actually the protein that i want to simulate consists of two amino acids: PHE and BOC BOC is an unusual amino acid as you know. It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE So that probably means you'll have to pay care to the [bonds] section in the .rtp file. The only bonds GROMACS knows about are the ones in the .rtp. They have to be right. The errors below look like you haven't done it right. I finally defined a residue BOC in opls .rtp file: [ BOC ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B -0.005 1 HA1opls_1400.060 1 HA2opls_1400.060 1 CBopls_1490.140 2 HB1opls_1400.060 2 CG1opls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_1450.885 7 Clopls_264 -1.000 7 CG2opls_071 -0.005 8 HG1opls_1400.060 8 HG2opls_1400.060 8 Copls_2350.700 9 Oopls_236 -0.700 9 the ending part of my PDB is: ... ATOM 38 HE2 PHE 2 -6.946 8.455 4.409 ATOM 39 CZ PHE 2 -5.456 10.015 4.624 ATOM 40 HZ PHE 2 -5.887 10.646 3.828 ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540 6.235 4.026 HA2 is missing here, per your .rtp ATOM 45 CB BOC 3 -1.797 4.794 2.924 ATOM 46 HB1 BOC 3 -2.244 3.809 3.204 ATOM 47 CG1 BOC 3 -2.976 5.730 2.589 ATOM 48 CG2 BOC 3 -0.935 4.544 1.698 ATOM 49 CD1 BOC 3 -1.231 3.466 0.845 ATOM 50 HD1 BOC 3 -2.070 2.790 1.081 ATOM 51 CD2 BOC 3 0.120 5.408 1.353 ATOM 52 HD2 BOC 3 0.357 6.277 1.986 ATOM 53 CE1 BOC 3
Re: [gmx-users] add a group to an amino acid
On 9/11/2010 9:09 PM, hengame fallah wrote: Dear Mark, I edited my pdb like this: ... ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540 6.235 4.026 ATOM 45 HA2 BOC 3 -0.172 4.511 4.360 ATOM 46 CB BOC 3 -1.797 4.794 2.924 ATOM 47 HB1 BOC 3 -2.244 3.809 3.204 ATOM 48 CG1 BOC 3 -2.976 5.730 2.589 ATOM 49 CD1 BOC 3 -1.231 3.466 0.845 ATOM 50 HD1 BOC 3 -2.070 2.790 1.081 ATOM 51 CD2 BOC 3 0.120 5.408 1.353 ATOM 52 HD2 BOC 3 0.357 6.277 1.986 ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312 ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964 ATOM 55 CE2 BOC 3 0.881 5.182 0.197 ATOM 56 HE2 BOC 3 1.706 5.870 -0.054 ATOM 57 CZ BOC 3 0.591 4.093 -0.639 ATOM 58 CG2 BOC 3 -0.935 4.544 1.698 ATOM 59 HG1 BOC 3 -3.530 5.331 1.707 ATOM 60 HG2 BOC 3 -3.708 5.729 3.431 ATOM 61 C BOC 3 -2.565 7.148 2.291 ATOM 62 O BOC 3 -2.716 8.035 3.131 ATOM 63 Cl BOC 3 1.525 3.816 -2.062 END and my .rtp file for [ BOC ] is: [ BOC ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B -0.005 1 HA1opls_1400.060 1 HA2opls_1400.060 1 CBopls_1490.140 2 HB1opls_1400.060 2 CG1opls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_1450.885 7 Clopls_264 -1.000 7 CG2opls_071 -0.005 8 HG1opls_1400.060 8 HG2opls_1400.060 8 Copls_2350.700 9 Oopls_236 -0.700 9 [ bonds ] N H NCA CA HA1 CA HA2 CACB CB HB1 CB CG1 CB CG2 CG1 CD1 CG1 CD2 CD1 HD1 CD1 CE1 CD2 HD2 CD2 CE2 CE1 HE1 CE1CZ CE2 HE2 CE2CZ CZCl CG2 HG1 CG2 HG2 CG2 C C O -C N and still i got that error! Fatal error: Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1 a) This structure is phenylalanine with *two* backbone methylene spacers, not the one you said in a previous email b) Your charge groups are wrong (e.g. number 2) c) Your charges are doubtful (CG1 is negative???) d) Your atom types are worth checking (should the two backbone methylene carbons have those types?) e) The atom ordering of the coordinate file and .rtp file need to match f) The atom coordinates do not correspond to the atom labels they are given - presumably you got another bunch of long bond warnings that you didn't include in your last email. Mark On Tue, Nov 9, 2010 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 9/11/2010 8:19 PM, hengame fallah wrote: Thanks Justin, actually the protein that i want to simulate consists of two amino acids: PHE and BOC BOC is an unusual amino acid as you know. It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE So that probably means you'll have to pay care to the [bonds] section in the .rtp file. The only bonds GROMACS knows about are the ones in the .rtp. They have to be right. The errors below look like you haven't done it right. I finally defined a residue BOC in opls .rtp file: [ BOC ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B -0.005 1 HA1opls_1400.060 1 HA2opls_1400.060 1 CBopls_1490.140 2 HB1opls_1400.060 2 CG1opls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_1450.885 7 Clopls_264 -1.000 7 CG2opls_071 -0.005 8 HG1opls_1400.060 8 HG2opls_1400.060 8 Copls_2350.700 9 Oopls_236 -0.700 9 the ending part of my PDB is: ... ATOM 38 HE2 PHE 2 -6.946 8.455 4.409 ATOM 39 CZ PHE 2 -5.456 10.015 4.624 ATOM 40
Re: [gmx-users] add a group to an amino acid
This is .rtp for [PHE] in opls: [ PHE ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_145 -0.115 7 HZopls_1460.115 7 Copls_2350.500 8 Oopls_236 -0.500 8 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CD2 HD2 CD2 CE2 CE1 HE1 CE1CZ CE2 HE2 CE2CZ CZHZ C O -C N and i got the charges by Gaussian. I'm very confused now [?] On Tue, Nov 9, 2010 at 2:13 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/11/2010 9:09 PM, hengame fallah wrote: Dear Mark, I edited my pdb like this: ... ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540 6.235 4.026 ATOM 45 HA2 BOC 3 -0.172 4.511 4.360 ATOM 46 CB BOC 3 -1.797 4.794 2.924 ATOM 47 HB1 BOC 3 -2.244 3.809 3.204 ATOM 48 CG1 BOC 3 -2.976 5.730 2.589 ATOM 49 CD1 BOC 3 -1.231 3.466 0.845 ATOM 50 HD1 BOC 3 -2.070 2.790 1.081 ATOM 51 CD2 BOC 3 0.120 5.408 1.353 ATOM 52 HD2 BOC 3 0.357 6.277 1.986 ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312 ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964 ATOM 55 CE2 BOC 3 0.881 5.182 0.197 ATOM 56 HE2 BOC 3 1.706 5.870 -0.054 ATOM 57 CZ BOC 3 0.591 4.093 -0.639 ATOM 58 CG2 BOC 3 -0.935 4.544 1.698 ATOM 59 HG1 BOC 3 -3.530 5.331 1.707 ATOM 60 HG2 BOC 3 -3.708 5.729 3.431 ATOM 61 C BOC 3 -2.565 7.148 2.291 ATOM 62 O BOC 3 -2.716 8.035 3.131 ATOM 63 Cl BOC 3 1.525 3.816 -2.062 END and my .rtp file for [ BOC ] is: [ BOC ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B -0.005 1 HA1opls_1400.060 1 HA2opls_1400.060 1 CBopls_1490.140 2 HB1opls_1400.060 2 CG1opls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_1450.885 7 Clopls_264 -1.000 7 CG2opls_071 -0.005 8 HG1opls_1400.060 8 HG2opls_1400.060 8 Copls_2350.700 9 Oopls_236 -0.700 9 [ bonds ] N H NCA CA HA1 CA HA2 CACB CB HB1 CB CG1 CB CG2 CG1 CD1 CG1 CD2 CD1 HD1 CD1 CE1 CD2 HD2 CD2 CE2 CE1 HE1 CE1CZ CE2 HE2 CE2CZ CZCl CG2 HG1 CG2 HG2 CG2 C C O -C N and still i got that error! Fatal error: Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1 a) This structure is phenylalanine with *two* backbone methylene spacers, not the one you said in a previous email b) Your charge groups are wrong (e.g. number 2) c) Your charges are doubtful (CG1 is negative???) d) Your atom types are worth checking (should the two backbone methylene carbons have those types?) e) The atom ordering of the coordinate file and .rtp file need to match f) The atom coordinates do not correspond to the atom labels they are given - presumably you got another bunch of long bond warnings that you didn't include in your last email. Mark On Tue, Nov 9, 2010 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/11/2010 8:19 PM, hengame fallah wrote: Thanks Justin, actually the protein that i want to simulate consists of two amino acids: PHE and BOC BOC is an unusual amino acid as you know. It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE So that probably means you'll have to pay care to the [bonds] section in the .rtp file. The only bonds GROMACS knows about are the ones in the .rtp. They have to be right. The errors
Re: [gmx-users] add a group to an amino acid
On 9/11/2010 10:10 PM, hengame fallah wrote: This is .rtp for [PHE] in opls: ...wherein all the charge groups are neutral, unlike yours for BOC. This will be fairly moot for a PME simulation, however. [ PHE ] [ atoms ] N opls_238 -0.500 1 H opls_241 0.300 1 CA opls_224B 0.140 1 HA opls_140 0.060 1 CB opls_149 -0.005 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_145 -0.115 2 CD1 opls_145 -0.115 3 HD1 opls_146 0.115 3 CD2 opls_145 -0.115 4 HD2 opls_146 0.115 4 CE1 opls_145 -0.115 5 HE1 opls_146 0.115 5 CE2 opls_145 -0.115 6 HE2 opls_146 0.115 6 CZ opls_145 -0.115 7 HZ opls_146 0.115 7 C opls_235 0.500 8 O opls_236 -0.500 8 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CD2 HD2 CD2 CE2 CE1 HE1 CE1 CZ CE2 HE2 CE2 CZ CZ HZ C O -C N and i got the charges by Gaussian. Is your method suitable for OPLSAA charges? (I don't know). See http://www.gromacs.org/Documentation/How-tos/Parameterization Regarding the copy of all these files that you sent me off-list, please refrain from doing so unless somebody requests them. I gave you an itemized list of things to fix, and you haven't addressed any of them that I could see. I'll add another item to the list - your .hdb format is wrong for the *two* hydrogens you're still telling it to try to add to CB, which is causing the fatal error. However you have many others issues to address as well. You're doing something that is advanced - be prepared to read chapter 5 of the manual closely! Mark I'm very confused now On Tue, Nov 9, 2010 at 2:13 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/11/2010 9:09 PM, hengame fallah wrote: Dear Mark, I edited my pdb like this: ... ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540 6.235 4.026 ATOM 45 HA2 BOC 3 -0.172 4.511 4.360 ATOM 46 CB BOC 3 -1.797 4.794 2.924 ATOM 47 HB1 BOC 3 -2.244 3.809 3.204 ATOM 48 CG1 BOC 3 -2.976 5.730 2.589 ATOM 49 CD1 BOC 3 -1.231 3.466 0.845 ATOM 50 HD1 BOC 3 -2.070 2.790 1.081 ATOM 51 CD2 BOC 3 0.120 5.408 1.353 ATOM 52 HD2 BOC 3 0.357 6.277 1.986 ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312 ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964 ATOM 55 CE2 BOC 3 0.881 5.182 0.197 ATOM 56 HE2 BOC 3 1.706 5.870 -0.054 ATOM 57 CZ BOC 3 0.591 4.093 -0.639 ATOM 58 CG2 BOC 3 -0.935 4.544 1.698 ATOM 59 HG1 BOC 3 -3.530 5.331 1.707 ATOM 60 HG2 BOC 3 -3.708 5.729 3.431 ATOM 61 C BOC 3 -2.565 7.148 2.291 ATOM 62 O BOC 3 -2.716 8.035 3.131 ATOM 63 Cl BOC 3 1.525 3.816 -2.062 END and my .rtp file for [ BOC ] is: [ BOC ] [ atoms ] N opls_238 -0.500 1 H opls_241 0.300 1 CA opls_224B -0.005 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 CB opls_149 0.140 2 HB1 opls_140 0.060 2 CG1 opls_145 -0.115 2 CD1 opls_145 -0.115 3 HD1 opls_146 0.115 3 CD2 opls_145 -0.115 4 HD2 opls_146 0.115 4 CE1 opls_145 -0.115 5 HE1 opls_146 0.115 5 CE2 opls_145 -0.115 6 HE2 opls_146 0.115 6 CZ opls_145 0.885 7 Cl opls_264 -1.000 7 CG2 opls_071 -0.005 8 HG1 opls_140 0.060 8 HG2 opls_140 0.060 8 C opls_235 0.700 9
[gmx-users] add a group to an amino acid
Hi, I'm using the OPLS force field. [ PHE ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_145 -0.115 7 HZopls_1460.115 7 Copls_2350.500 8 Oopls_236 -0.500 8 I want to attach CL atom instead of HZ i made my pdb but when i use pdb2gmx, it adds HZ automatically in gro and top files. What should i do to get rid of this HZ and attach CL instead. (I edited top and gro files and remove HZ from them, it seemed to work properly at first, but when i tried to do energy minimization, it had errors in top file and i realized that it couldn't recognized the bond between CL and CZ): ERROR 1 [file topol.top, line 150]: No default Bond types ERROR 2 [file topol.top, line 422]: No default Angle types ERROR 3 [file topol.top, line 423]: No default Angle types *topol.top:* ... 58 opls_146 3PHE HE2 22 0.115 1.008; qtot 0.9 59 opls_145 3PHE CZ 23 -0.115 12.011 ; qtot 0.785 60 opls_271 3PHE C 240.7 12.011 ; qtot 1.6 61 opls_272 3PHE O1 24 -0.815.9994; qtot 0.8 62 opls_272 3PHE O2 24 -0.815.9994; qtot 0 63 opls_135 4EtOHCB 25 -0.18 12.011; qtot -0.18 64 opls_140 4EtOHHB1 25 0.06 1.008 ; qtot -0.12 65 opls_140 4EtOHHB2 25 0.06 1.008 ; qtot -0.06 66 opls_401 5CLCL 26 -1 35.453 ; qtot -1.06 ... [ bonds ] ... 5966 1 6061 1 6062 1 6364 1 6365 1 ... [ angles ] ... 585759 1 555957 1 555966 1 575966 1 456061 1 456062 1 616062 1 646365 1 ... -- 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] add a group to an amino acid
hengame fallah wrote: Hi, I'm using the OPLS force field. [ PHE ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_145 -0.115 2 CD1opls_145 -0.115 3 HD1opls_1460.115 3 CD2opls_145 -0.115 4 HD2opls_1460.115 4 CE1opls_145 -0.115 5 HE1opls_1460.115 5 CE2opls_145 -0.115 6 HE2opls_1460.115 6 CZopls_145 -0.115 7 HZopls_1460.115 7 Copls_2350.500 8 Oopls_236 -0.500 8 I want to attach CL atom instead of HZ i made my pdb but when i use pdb2gmx, it adds HZ automatically in gro and top files. What should i do to get rid of this HZ and attach CL instead. If the .rtp entry says to build PHE with those constituent atoms, it will do so. You can make a custom .rtp entry that has CL instead of HZ. (I edited top and gro files and remove HZ from them, it seemed to work properly at first, but when i tried to do energy minimization, it had errors in top file and i realized that it couldn't recognized the bond between CL and CZ): ERROR 1 [file topol.top, line 150]: No default Bond types ERROR 2 [file topol.top, line 422]: No default Angle types ERROR 3 [file topol.top, line 423]: No default Angle types All of these errors indicate that OPLS cannot accommodate such a species. Making ad hoc changes to the topology often does this. Look at what these lines contain and you will be able to identify the relevant parameters that are missing. snip 66 opls_401 5CLCL 26 -1 35.453 ; qtot -1.06 I would seriously question the validity of doing this. Is it really correct to put (essentially) a Cl- ion on a Phe ring and call it correct? Proper parameterization is a very challenging task, and I doubt what you've proposed here is valid. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin ... [ bonds ] ... 5966 1 6061 1 6062 1 6364 1 6365 1 ... [ angles ] ... 585759 1 555957 1 555966 1 575966 1 456061 1 456062 1 616062 1 646365 1 ... -- 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 -- 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
