maria goranovic wrote:
Sorry for the incomplete reply. version 4.5.3, command: pdb2gmx -f guan.pdb -ignhI tried using -ter, but that did not help.
It appears that pdb2gmx is not equipped to handle the case of an isolated nucleotide. Keep in mind that pdb2gmx is intended for use with repeat building blocks of monomers, not isolated molecules. The default behavior is to assign a 5' end with no phosphate (i.e. RG rather than pRG). Attempting to choose "None" for a terminus leaves an incomplete phosphate group (i.e. PO3 instead of PO4) and thus a fatal error about a "dangling bond." I'm guessing this has been your experience?
There are two potential solutions:1. Write an .rtp entry of a complete, custom RG nucleotide with the desired PO4 5' end.
2. Write a new entry in rna.n.tdb that adds another phosphate oxygen and adjusts charges appropriately by replacing the existing O and P atoms, at least.
-Justin
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 10.00000On Tue, Mar 22, 2011 at 2:09 PM, Mark Abraham <mark.abra...@anu.edu.au <mailto: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? Markjust bumping, maria On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic <mariagorano...@gmail.com <mailto: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 1ATOM 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 HOf 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 <mailto:mark.abra...@anu.edu.au>> wrote: On 19/03/11, *maria goranovic * <mariagorano...@gmail.com <mailto: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 evengive 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 simpleworkflow 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_Field Your 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 <mailto: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 <mailto: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 <mailto: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 <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen
-- ======================================== 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.
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