Just an update, I decided to create a new residue for an isolated GMP. Well, not really, because I used pdb2gmx to output a topology of a dimer, and then modified it carefully to extract the topology of a phosphorylated GTP.
thank you ! On Tue, Mar 22, 2011 at 2:52 PM, maria goranovic <[email protected]>wrote: > the gro file was the input. I am attaching a pdb as well > > CRYST1 100.0 100.0 100.0 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 9 O3' G A 4 1.869 2.669 1.934 1.00 0.00 > O > ATOM 10 C2' G A 4 0.136 1.413 0.721 1.00 0.00 > C > ATOM 11 O2' G A 4 -0.363 2.696 0.397 1.00 0.00 > O > ATOM 12 C1' G A 4 0.241 0.597 -0.574 1.00 0.00 > C > ATOM 13 N9 G A 4 -0.450 -0.705 -0.438 1.00 0.00 > N > ATOM 14 C8 G A 4 0.075 -1.954 -0.237 1.00 0.00 > C > ATOM 15 N7 G A 4 -0.808 -2.911 -0.197 1.00 0.00 > N > ATOM 16 C5 G A 4 -2.017 -2.251 -0.377 1.00 0.00 > C > ATOM 17 C6 G A 4 -3.346 -2.767 -0.450 1.00 0.00 > C > ATOM 18 O6 G A 4 -3.705 -3.941 -0.398 1.00 0.00 > O > ATOM 19 N1 G A 4 -4.299 -1.762 -0.593 1.00 0.00 > N > ATOM 20 C2 G A 4 -4.002 -0.413 -0.682 1.00 0.00 > C > ATOM 21 N2 G A 4 -5.023 0.438 -0.804 1.00 0.00 > N > ATOM 22 N3 G A 4 -2.751 0.071 -0.652 1.00 0.00 > N > ATOM 23 C4 G A 4 -1.809 -0.897 -0.499 1.00 0.00 > C > ATOM 24 H5' G A 4 4.293 1.204 -0.960 1.00 0.00 > H > ATOM 25 H5'' G A 4 4.269 1.819 0.696 1.00 0.00 > H > ATOM 26 H4' G A 4 2.217 2.395 -0.623 1.00 0.00 > H > ATOM 27 H3' G A 4 1.819 0.589 1.792 1.00 0.00 > H > ATOM 28 H2' G A 4 -0.503 0.940 1.465 1.00 0.00 > H > ATOM 29 HO2' G A 4 -1.301 2.614 0.210 1.00 0.00 > H > ATOM 30 H1' G A 4 -0.225 1.145 -1.393 1.00 0.00 > H > ATOM 31 H8 G A 4 1.129 -2.132 -0.139 1.00 0.00 > H > ATOM 32 H1 G A 4 -5.265 -2.065 -0.635 1.00 0.00 > H > 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 > END > > > On Tue, Mar 22, 2011 at 2:43 PM, Daniel Adriano Silva M < > [email protected]> wrote: > >> 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 <[email protected]> >> >>> 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 >>> <[email protected]>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 < >>>> [email protected]> 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 < >>>>> [email protected]> wrote: >>>>> >>>>>> >>>>>> >>>>>> On 19/03/11, *maria goranovic * <[email protected]> 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 [email protected] >>>>>> 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 [email protected]. >>>>>> 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 [email protected] >>>> 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 [email protected]. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> >>> >>> -- >>> Maria G. >>> Technical University of Denmark >>> Copenhagen >>> >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
