Re: [gmx-users] tfe.gro
Thank you very much ABEL Stephane. On Tue, Nov 30, 2010 at 3:28 PM, ABEL Stephane 175950 stephane.a...@cea.frwrote: Hi Hengameh Below, my TFE.gro (with the atom names for CHARMM Cgenff) i used it previously for md. You can easely translated in others ff you use 9 1TFE O11 0.397 1.386 1.484 0.4892 -0.3653 -0.3242 1TFEHO12 0.446 1.346 1.557 0.8382 -0.5070 -0.6322 1TFEH113 0.334 1.332 1.295 1.2033 -0.8553 -0.5343 1TFEH124 0.436 1.209 1.380 2.6521 2.1877 0.2597 1TFE C15 0.355 1.285 1.393 0. -0.4118 -0.0512 1TFEF216 0.186 1.128 1.352 0.1711 -0.0500 0.0270 1TFEF227 0.117 1.302 1.447 -0.1931 0.5088 -0.2066 1TFEF238 0.235 1.159 1.557 0.0214 0.0727 -0.2415 1TFE C29 0.224 1.222 1.439 -0.3522 0.2823 -0.0958 and the TFE.pdb file used to obtain the gro file above ATOM 1 O1 TFE 1 1.9123 -0.2235 0. ATOM 2 HO1 TFE 1 2.7589 0.2000 0. ATOM 3 H11 TFE 1 0.9282 1.3623 -0.8827 ATOM 4 H12 TFE 1 0.9282 1.3623 0.8827 ATOM 5 C1 TFE 1 -0.4189 0.0062 -0. ATOM 6 F21 TFE 1 -1.4055 0.8930 -0. ATOM 7 F22 TFE 1 -0.5650 -0.7556 -1.0660 ATOM 8 F23 TFE 1 -0.5650 -0.7556 1.0660 ATOM 9 C2 TFE 1 0.9031 0.7318 -0. Hope it helps Stefane -- 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 -- Hengameh Fallah M.Sc. Computational Chemistry -- 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] tfe.gro
Hi, Does anyone have the tfe.gro for solvent box? I have the tfe.itp file in /usr/share/gromacs/top/ directory. [ atoms ] 1 C 1 TFE C 1 0.74 2 F 1 TFE F 1-0.25 3 F 1 TFE F 1-0.25 4 F 1 TFE F 1-0.25 5 CH2 1 TFE CH2 10.25 6 OA1 TFE OA 1-0.65 7 HO1 TFE HO 1 0.41 I think that the .gro file for ethanol would help me, too if someone has it. Thanks Hengameh -- 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
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
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
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
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
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
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
[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
