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 ] 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 O opls_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 ] >> 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 >> >> 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 5 CL CL 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 ] >> ... >> 59 66 1 >> 60 61 1 >> 60 62 1 >> 63 64 1 >> 63 65 1 >> ... >> [ angles ] >> ... >> 58 57 59 1 >> 55 59 57 1 >> 55 59 66 1 >> 57 59 66 1 >> 45 60 61 1 >> 45 60 62 1 >> 61 60 62 1 >> 64 63 65 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 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 >
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