Hi, Is this your input? (a GRO file?). Can you paste the PDB corresponding to the RNA nucleotide that you are interested on? I think the file may be small enough to paste it here so someone can try to reproduce what is happening to you.
Daniel 2011/3/22 maria goranovic <mariagorano...@gmail.com> > Sorry for the incomplete reply. > version 4.5.3, > command: pdb2gmx -f guan.pdb -ignh > I tried using -ter, but that did not help. > > > input coordinate file, pulled out from an RNA molecule. > > Gromacs Runs On Most of All Computer Systems > 34 > 1G P 1 5.549 4.916 5.071 > 1G OP1 2 5.642 5.026 5.105 > 1G OP2 3 5.537 4.800 5.162 > 1G O5' 4 5.401 4.979 5.051 > 1G C5' 5 5.382 5.110 5.001 > 1G C4' 6 5.232 5.143 4.988 > 1G O4' 7 5.162 5.045 4.914 > 1G C3' 8 5.158 5.148 5.121 > 1G O3' 9 5.187 5.267 5.193 > 1G C2' 10 5.014 5.141 5.072 > 1G O2' 11 4.964 5.270 5.040 > 1G C1' 12 5.024 5.060 4.943 > 1G N9 13 4.955 4.930 4.956 > 1G C8 14 5.008 4.805 4.976 > 1G N7 15 4.919 4.709 4.980 > 1G C5 16 4.798 4.775 4.962 > 1G C6 17 4.665 4.723 4.955 > 1G O6 18 4.630 4.606 4.960 > 1G N1 19 4.570 4.824 4.941 > 1G C2 20 4.600 4.959 4.932 > 1G N2 21 4.498 5.044 4.920 > 1G N3 22 4.725 5.007 4.935 > 1G C4 23 4.819 4.910 4.950 > 1G H5' 24 5.429 5.120 4.904 > 1G H5'' 25 5.427 5.182 5.070 > 1G H4' 26 5.222 5.240 4.938 > 1G H3' 27 5.182 5.059 5.179 > 1G H2' 28 4.950 5.094 5.146 > 1G HO2' 29 4.870 5.261 5.021 > 1G H1' 30 4.978 5.115 4.861 > 1G H8 31 5.113 4.787 4.986 > 1G H1 32 4.474 4.794 4.936 > 1G H21 33 4.403 5.010 4.918 > 1G H22 34 4.516 5.143 4.912 > 10.00000 10.00000 10.00000 > > > On Tue, Mar 22, 2011 at 2:09 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 22/03/2011 8:15 PM, maria goranovic wrote: >> >> is this a bug of some kind then? someone ? anyone? >> >> >> It's still hard to say. I asked you for your GROMACS version and input >> coordinate file, and you didn't give us either (in full). While you're >> there, what pdb2gmx command did you use? >> >> Mark >> >> >> just bumping, >> >> maria >> >> On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic < >> mariagorano...@gmail.com> wrote: >> >>> Here are the contents of my input coordinate file. >>> >>> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 >>> ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00 >>> P >>> ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00 >>> O >>> ATOM 3 OP2 G A 4 5.367 -1.998 1.624 1.00 0.00 >>> O >>> ATOM 4 O5' G A 4 4.010 -0.213 0.513 1.00 0.00 >>> O >>> ATOM 5 C5' G A 4 3.816 1.098 0.014 1.00 0.00 >>> C >>> ATOM 6 C4' G A 4 2.324 1.432 -0.121 1.00 0.00 >>> C >>> ATOM 7 O4' G A 4 1.623 0.448 -0.862 1.00 0.00 >>> O >>> ATOM 8 C3' G A 4 1.584 1.482 1.211 1.00 0.00 >>> C >>> .... >>> ATOM 33 H21 G A 4 -5.974 0.099 -0.815 1.00 0.00 >>> H >>> ATOM 34 H22 G A 4 -4.841 1.428 -0.876 1.00 0.00 >>> H >>> >>> >>> Of course it would be best if pdb2gmx worked as it is if I just have >>> a single nucleotide, and not a chain? >>> >>> >>> Here, I am wondering if the above problem is occurring because pdb2gmx >>> is not being able to deal with an isolated nucleotide (while it might be >>> able to deal with an polymer) >>> >>> Maria >>> >>> >>> On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham >>> <mark.abra...@anu.edu.au>wrote: >>> >>>> >>>> >>>> On 19/03/11, *maria goranovic * <mariagorano...@gmail.com> wrote: >>>> >>>> Dear All >>>> >>>> I am trying to generate a topology for guanosine monophosphate: i.e. >>>> an RNA base with a phosphate at the 5' Carbon. I tried to read in a pdb >>>> file >>>> containing all atoms, and used pdb2gmx with CHARMM. However, the output >>>> coordinate file has no phosphate group on it. Why does the phosphate >>>> disappear, and why does pdb2gmx not even give me a warning? >>>> >>>> >>>> That does sound suspicious, but it's hard to say what went wrong. What >>>> GROMACS version was it, and what were the contents of your input coordinate >>>> file? >>>> >>>> >>>> Assuming that a molecule like GMP does not have a topology, I am >>>> guessing I might have to make a new residue within CHARMM. that should not >>>> be too much work because there is no new angle/dihedral/bond/atom type to >>>> be >>>> be added. Can someone please help me with a simple workflow so I do not >>>> miss >>>> something important? >>>> >>>> >>>> The procedure is outlined here: >>>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_FieldYour >>>> case should be a reasonably straightforward exercise in assigning >>>> sensible atom types from the pre-existing options. >>>> >>>> >>>> >>>> >>>> Mark >>>> -- >>>> 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 >>>> >>> >>> >>> >>> -- >>> Maria G. >>> Technical University of Denmark >>> Copenhagen >>> >> >> >> >> -- >> Maria G. >> Technical University of Denmark >> Copenhagen >> >> >> >> -- >> 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 >> > > > > -- > Maria G. > Technical University of Denmark > Copenhagen > > -- > 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