Yes I finally got it too. However I've managed to change correctly the atoms names for the first residue and now it is complaining for the others. This is my pdb file
ATOM 1 CA ACE 1 -3.547 1.520 1.054 ATOM 2 H1 ACE 1 -3.081 0.536 0.999 ATOM 3 H2 ACE 1 -3.437 0.016 0.110 ATOM 4 H3 ACE 1 -3.348 -0.041 1.883 ATOM 5 C ACE 1 -1.570 0.683 0.929 ATOM 6 O ACE 1 -1.051 1.800 0.938 ATOM 7 N ALA 2 -0.862 -0.446 0.851 ATOM 8 H ALA 2 -1.368 -1.322 0.859 ATOM 9 CA ALA 2 0.607 -0.509 0.828 ATOM 10 HA ALA 2 0.997 0.272 1.484 ATOM 11 CB ALA 2 1.025 -1.867 1.412 ATOM 12 1HB ALA 2 2.113 -1.918 1.485 ATOM 13 2HB ALA 2 0.676 -2.677 0.770 ATOM 14 3HB ALA 2 0.604 -1.990 2.411 ATOM 15 C ALA 2 1.238 -0.262 -0.565 ATOM 16 O ALA 2 2.465 -0.181 -0.678 ATOM 17 N NAC 3 0.423 -0.139 -1.620 ATOM 18 H NAC 3 -0.569 -0.212 -1.447 ATOM 19 CH3 NAC 3 0.860 0.098 -2.992 ATOM 20 HA1 NAC 3 1.413 1.037 -3.050 ATOM 21 HA2 NAC 3 1.506 -0.718 -3.323 ATOM 22 HA3 NAC 3 -0.006 0.155 -3.652 Do you know how to change the other residues or where I can find a library that has this information? Thanks 2012/2/17 Mark Abraham <mark.abra...@anu.edu.au>: > On 17/02/2012 9:14 PM, francesca vitalini wrote: >> >> I tried, but apparently the atom that it is looking for exist already >> in the rtp file!! >> >> this is the error >> >> Program pdb2gmx, VERSION 3.3.1 >> Source code file: pdb2gmx.c, line: 383 >> >> Fatal error: >> Atom CH3 in residue ACE 1 not found in rtp entry with 3 atoms >> while sorting atoms > > > CH3 is the atom type for the terminal C, CA is its name. I think you have > misnamed your atoms in your coordinate file. > > Mark > > >> >> >> and this is the rtp file for residue ACE >> >> [ ACE ] >> [ atoms ] >> CA CH3 0.000 0 >> C C 0.450 1 >> O O -0.450 1 >> [ bonds ] >> C CA gb_27 >> C O gb_5 >> C +N gb_19 >> [ angles ] >> CA C +N ga_19 >> O C +N ga_33 >> [ impropers ] >> C CA +N O gi_1 >> >> [ NH2 ] >> [ atoms ] >> N NT -0.83 0 >> H1 H 0.415 0 >> H2 H 0.415 0 >> [ bonds ] >> N H1 gb_2 >> N H2 gb_2 >> -C N gb_9 >> [ angles ] >> -O -C N ga_33 >> -CA -C N ga_19 >> -C N H1 ga_23 >> -C N H2 ga_23 >> H1 N H2 ga_24 >> [ dihedrals ] >> -CA -C N H1 gd_14 >> [ impropers ] >> -C -O N -CA gi_1 >> N H H -C gi_1 >> >> >> Any help? >> >> >> >> 2012/2/16 Justin A. Lemkul<jalem...@vt.edu>: >>> >>> >>> francesca vitalini wrote: >>>> >>>> Do you mean that I can just use the new version of pdb2gmx than change >>>> the included forcefield and in case the name of the atoms and it >>>> should work? >>>> >>> You still have to fix the incorrect atom name(s), regardless of version. >>> You can use a new version to make use of pdb2gmx -ter, if necessary. >>> Otherwise, your version should work for what you need. >>> >>> -Justin >>> >>> >>>> 2012/2/16 Justin A. Lemkul<jalem...@vt.edu>: >>>>> >>>>> >>>>> francesca vitalini wrote: >>>>>> >>>>>> Hi all! >>>>>> I'm trying to create a topology file from the pdb using the pdb2gmx >>>>>> command of gromacs 3.3.1 but I'm encountering some issues. I should >>>>>> use the flag -tar in order to select interactively the termini, but >>>>>> with the old version of gromacs this is not implemented and I cannot >>>>>> use a new one because I need the reverse transformation tool which is >>>>>> only implemented in that version. >>>>> >>>>> >>>>> The topology format is largely unaffected by differences in version. A >>>>> few >>>>> moments with a text editor to fix the #include statements written by a >>>>> version in the 4.5.x series would solve any problems. >>>>> >>>>> >>>>>> Here it is the pdb I'm using >>>>>> >>>>>> REMARK >>>>>> ATOM 1 1HH3 ACE 1 -3.547 1.520 1.054 >>>>>> ATOM 2 CH3 ACE 1 -3.081 0.536 0.999 >>>>>> ATOM 3 2HH3 ACE 1 -3.437 0.016 0.110 >>>>>> ATOM 4 3HH3 ACE 1 -3.348 -0.041 1.883 >>>>>> ATOM 5 C ACE 1 -1.570 0.683 0.929 >>>>>> ATOM 6 O ACE 1 -1.051 1.800 0.938 >>>>>> ATOM 7 N ALA 2 -0.862 -0.446 0.851 >>>>>> ATOM 8 H ALA 2 -1.368 -1.322 0.859 >>>>>> ATOM 9 CA ALA 2 0.607 -0.509 0.828 >>>>>> ATOM 10 HA ALA 2 0.997 0.272 1.484 >>>>>> ATOM 11 CB ALA 2 1.025 -1.867 1.412 >>>>>> ATOM 12 1HB ALA 2 2.113 -1.918 1.485 >>>>>> ATOM 13 2HB ALA 2 0.676 -2.677 0.770 >>>>>> ATOM 14 3HB ALA 2 0.604 -1.990 2.411 >>>>>> ATOM 15 C ALA 2 1.238 -0.262 -0.565 >>>>>> ATOM 16 O ALA 2 2.465 -0.181 -0.678 >>>>>> ATOM 17 N NAC 3 0.423 -0.139 -1.620 >>>>>> ATOM 18 H NAC 3 -0.569 -0.212 -1.447 >>>>>> ATOM 19 CH3 NAC 3 0.860 0.098 -2.992 >>>>>> ATOM 20 1HH3 NAC 3 1.413 1.037 -3.050 >>>>>> ATOM 21 2HH3 NAC 3 1.506 -0.718 -3.323 >>>>>> ATOM 22 3HH3 NAC 3 -0.006 0.155 -3.652 >>>>>> TER >>>>>> END >>>>>> >>>>>> >>>>>> And this is the pdb2gmx command >>>>>> path/pdb2gmx -ignh -missing -f struct1-1.pdb -p ala.top -o ala.gro >>>>>> >>>>>> >>>>>> I use the gromos9653a6 forcefield and the spc water model >>>>>> >>>>>> And this is the error I get >>>>>> >>>>>> There are 2 donors and 2 acceptors >>>>>> There are 2 hydrogen bonds >>>>>> ------------------------------------------------------- >>>>>> Program pdb2gmx, VERSION 3.3.1 >>>>>> Source code file: pdb2gmx.c, line: 383 >>>>>> >>>>>> Fatal error: >>>>>> Atom CH3 in residue ACE 1 not found in rtp entry with 3 atoms >>>>>> while sorting atoms >>>>>> ------------------------------------------------------- >>>>>> >>>>>> Any suggestions? >>>>> >>>>> >>>>> Check the .rtp file - your atom is named in a way that is inconsistent >>>>> with >>>>> what the force field expects. >>>>> >>>>> -Justin >>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> 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 >>>> >>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> 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 >> >> >> > > -- > 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 -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412 -- 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
