This is .rtp for [PHE] in opls: [ 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. 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 > O opls_236 -0.700 9 > [ bonds ] > N H > N CA > CA HA1 > CA HA2 > CA CB > CB HB1 > CB CG1 > CB CG2 > CG1 CD1 > CG1 CD2 > CD1 HD1 > CD1 CE1 > CD2 HD2 > CD2 CE2 > CE1 HE1 > CE1 CZ > CE2 HE2 > CE2 CZ > CZ Cl > 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>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 ] >> 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 >> >> >> 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? >> >> >> > > -- > 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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