Hi Albert,
The charmmlipid2amber.x script expects very specific input. It is not
designed to be bullet proof. It expects output from the Charmm lipid
builder. If your pdb is not in that specific format then you will have to
manually convert it. How specifically did you get your initial lipid pdb
file?
Ben can answer more when he gets in but I also suspect, although I haven't
looked at the script in a while, that it is not designed to work with pdbs
containing protein and waters. You will need to remove these from the file,
run the script to convert the lipid naming and then manually put the water
and protein back in. These are pretty advanced calculations so you will need
to do a lot of the leg work yourself I'm afraid. It will be quite a while
until everything can be properly automated I'm afraid.
All the best
Ross
> -----Original Message-----
> From: Albert [mailto:mailmd2011.gmail.com]
> Sent: Tuesday, May 08, 2012 6:48 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] charmmlipid2amber.x error
>
> hello David:
> I found a very strange thing:
>
> if I isolate the lipis into a individual pdb file, and this command
> works fine.... However, ti split the lipids into different part:
>
> TOM 12798 C12 PA 388 2.420 50.090 70.990 1.00 0.00
> MEMB
> ATOM 12799 H2R PA 388 1.390 49.990 70.610 1.00 0.00
> MEMB
> ATOM 12800 H2S PA 388 2.950 49.130 70.880 1.00 0.00
> MEMB
> ATOM 12848 C13 PA 388 3.200 51.190 70.230 1.00 0.00
> MEMB
> ATOM 12849 H3R PA 388 4.130 51.410 70.810 1.00 0.00
> MEMB
> ATOM 12850 H3S PA 388 2.620 52.130 70.180 1.00 0.00
> MEMB
> ATOM 12851 C14 PA 388 3.640 50.790 68.820 1.00 0.00
> MEMB
> ATOM 12852 H4R PA 388 3.930 49.720 68.800 1.00 0.00
> MEMB
> ATOM 12853 H4S PA 388 4.570 51.390 68.620 1.00 0.00
> MEMB
> ATOM 12854 C15 PA 388 2.670 51.100 67.670 1.00 0.00
> MEMB
> ATOM 12855 H5R PA 388 2.310 52.140 67.770 1.00 0.00
> MEMB
> ATOM 12856 H5S PA 388 1.790 50.420 67.720 1.00 0.00
> MEMB
> ATOM 12857 C16 PA 388 3.400 50.950 66.330 1.00 0.00
> MEMB
> ATOM 12858 H6R PA 388 3.690 49.890 66.200 1.00 0.00
> MEMB
> ATOM 12859 H6S PA 388 4.330 51.550 66.390 1.00 0.00
> MEMB
> ATOM 12860 C17 PA 388 2.650 51.420 65.070 1.00 0.00
> MEMB
> ATOM 12861 H7R PA 388 2.480 52.520 65.150 1.00 0.00
> MEMB
> ATOM 12862 H7S PA 388 1.670 50.910 65.010 1.00 0.00
> MEMB
> ATOM 12863 C18 PA 388 3.480 51.150 63.810 1.00 0.00
> MEMB
> ATOM 12864 H8R PA 388 3.470 50.050 63.640 1.00 0.00
> MEMB
> ATOM 12865 H8S PA 388 4.520 51.490 64.020 1.00 0.00
> MEMB
> ATOM 12866 C19 PA 388 3.080 51.820 62.500 1.00 0.00
> MEMB
> ATOM 12867 H9R PA 388 3.060 52.920 62.660 1.00 0.00
> MEMB
> ATOM 12868 H9S PA 388 2.060 51.470 62.220 1.00 0.00
> MEMB
> ATOM 12869 0C31 POPE 388 4.060 51.500 61.360 1.00 0.00
> MEMB
> ATOM 12870 H10R PA 388 4.090 50.400 61.200 1.00 0.00
> MEMB
> ATOM 12871 H10S PA 388 5.080 51.800 61.680 1.00 0.00
> MEMB
> ATOM 12872 1C31 POPE 388 3.730 52.170 60.020 1.00 0.00
> MEMB
> ATOM 12873 H11R PA 388 3.960 53.250 60.110 1.00 0.00
> MEMB
> ATOM 12874 H11S PA 388 2.650 52.040 59.800 1.00 0.00
> MEMB
> ATOM 12875 2C31 POPE 388 4.520 51.580 58.840 1.00 0.00
> MEMB
> ATOM 12876 H12R PA 388 4.160 50.540 58.680 1.00 0.00
> MEMB
> ATOM 12877 H12S PA 388 5.580 51.550 59.110 1.00 0.00
> MEMB
> ATOM 12878 3C31 POPE 388 4.450 52.300 57.490 1.00 0.00
> MEMB
> ATOM 12879 H13R PA 388 5.370 52.920 57.360 1.00 0.00
> MEMB
> ATOM 12880 H13S PA 388 3.590 52.990 57.460 1.00 0.00
> MEMB
> ATOM 12881 4C31 POPE 388 4.310 51.320 56.320 1.00 0.00
> MEMB
> ATOM 12882 H14R PA 388 3.330 50.800 56.430 1.00 0.00
> MEMB
> ATOM 12883 H14S PA 388 5.110 50.550 56.370 1.00 0.00
> MEMB
> ATOM 12884 5C31 POPE 388 4.360 52.010 54.960 1.00 0.00
> MEMB
> ATOM 12885 H15R PA 388 3.730 52.930 54.990 1.00 0.00
> MEMB
> ATOM 12886 H15S PA 388 3.880 51.310 54.230 1.00 0.00
> MEMB
> ATOM 12887 6C31 POPE 388 5.770 52.340 54.470 1.00 0.00
> MEMB
> ATOM 12888 H16R PA 388 6.380 51.410 54.410 1.00 0.00
> MEMB
> ATOM 12889 H16S PA 388 6.270 53.050 55.160 1.00 0.00
> MEMB
> ATOM 12890 H16T PA 388 5.730 52.800 53.460 1.00 0.00
> MEMB
> ATOM 12766 N31 PE 388 0.470 56.020 78.950 1.00 0.00
> MEMB
> ATOM 12767 HN1A PE 388 1.250 55.950 79.640 1.00 0.00
> MEMB
> ATOM 12768 HN1B PE 388 -0.330 56.520 79.400 1.00 0.00
> MEMB
> ATOM 12769 HN1C PE 388 0.840 56.640 78.170 1.00 0.00
> MEMB
> ATOM 12770 C32 PE 388 0.180 54.670 78.380 1.00 0.00
> MEMB
> ATOM 12771 H2A PE 388 -0.280 54.810 77.390 1.00 0.00
> MEMB
> ATOM 12772 H2B PE 388 -0.540 54.160 79.050 1.00 0.00
> MEMB
> ATOM 12773 C31 PE 388 1.490 53.880 78.290 1.00 0.00
> MEMB
> ATOM 12774 H1A PE 388 1.270 52.870 77.870 1.00 0.00
> MEMB
> ATOM 12775 H1B PE 388 1.890 53.740 79.320 1.00 0.00
> MEMB
> ATOM 12776 P31 PE 388 3.930 54.130 77.380 1.00 0.00
> MEMB
> ATOM 12777 O33 PE 388 4.700 55.090 76.570 1.00 0.00
> MEMB
> ATOM 12778 O34 PE 388 4.440 53.810 78.740 1.00 0.00
> MEMB
> ATOM 12779 O31 PE 388 3.710 52.760 76.600 1.00 0.00
> MEMB
> ATOM 12780 O32 PE 388 2.420 54.580 77.460 1.00 0.00
> MEMB
> ATOM 12781 C3 PE 388 4.830 52.050 76.050 1.00 0.00
> MEMB
> ATOM 12782 HA PE 388 5.020 51.130 76.640 1.00 0.00
> MEMB
> ATOM 12783 HB PE 388 5.780 52.650 76.080 1.00 0.00
> MEMB
> ATOM 12784 C2 PE 388 4.570 51.670 74.560 1.00 0.00
> MEMB
> ATOM 12785 HX PE 388 5.550 51.430 74.090 1.00 0.00
> MEMB
> ATOM 12786 O21 PE 388 3.920 52.740 73.850 1.00 0.00
> MEMB
> ATOM 12787 C21 PE 388 4.730 53.780 73.650 1.00 0.00
> MEMB
> ATOM 12788 O22 PE 388 5.920 53.820 73.920 1.00 0.00
> MEMB
> ATOM 12792 C1 PE 388 3.700 50.390 74.440 1.00 0.00
> MEMB
> ATOM 12793 HR PE 388 2.750 50.510 75.010 1.00 0.00
> MEMB
> ATOM 12794 HS PE 388 4.250 49.560 74.930 1.00 0.00
> MEMB
> ATOM 12795 O11 PE 388 3.500 50.050 73.050 1.00 0.00
> MEMB
> ATOM 12796 C11 PE 388 2.350 50.390 72.490 1.00 0.00
> MEMB
> ATOM 12797 O12 PE 388 1.380 50.850 73.070 1.00 0.00
> MEMB
> ATOM 12789 C12 OL 388 3.980 54.910 72.980 1.00 0.00
> MEMB
> ATOM 12790 H2R OL 388 4.720 55.700 72.760 1.00 0.00
> MEMB
> ATOM 12791 H2S OL 388 3.240 55.280 73.730 1.00 0.00
> MEMB
> ATOM 12801 C13 OL 388 3.250 54.530 71.680 1.00 0.00
> MEMB
> ATOM 12802 H3R OL 388 2.390 55.230 71.590 1.00 0.00
> MEMB
> ATOM 12803 H3S OL 388 2.840 53.500 71.750 1.00 0.00
> MEMB
> ATOM 12804 C14 OL 388 4.120 54.720 70.430 1.00 0.00
> MEMB
> ATOM 12805 H4R OL 388 4.850 53.880 70.380 1.00 0.00
> MEMB
> ATOM 12806 H4S OL 388 4.690 55.670 70.530 1.00 0.00
> MEMB
> ATOM 12807 C15 OL 388 3.310 54.790 69.130 1.00 0.00
> MEMB
> ATOM 12808 H5R OL 388 2.700 55.720 69.130 1.00 0.00
> MEMB
> ATOM 12809 H5S OL 388 2.630 53.930 69.070 1.00 0.00
> MEMB
> ATOM 12810 C16 OL 388 4.220 54.800 67.890 1.00 0.00
> MEMB
> ATOM 12811 H6R OL 388 4.900 53.930 67.980 1.00 0.00
> MEMB
> ATOM 12812 H6S OL 388 4.840 55.720 67.900 1.00 0.00
> MEMB
> ATOM 12813 C17 OL 388 3.460 54.650 66.570 1.00 0.00
> MEMB
> ATOM 12814 H7R OL 388 2.520 54.120 66.790 1.00 0.00
> MEMB
> ATOM 12815 H7S OL 388 4.030 53.990 65.880 1.00 0.00
> MEMB
> ATOM 12816 C18 OL 388 3.160 55.980 65.860 1.00 0.00
> MEMB
> ATOM 12817 H8R OL 388 2.730 56.680 66.620 1.00 0.00
> MEMB
> ATOM 12818 H8S OL 388 2.380 55.820 65.100 1.00 0.00
> MEMB
> ATOM 12819 C19 OL 388 4.400 56.590 65.240 1.00 0.00
> MEMB
> ATOM 12820 H9R OL 388 5.050 57.110 65.950 1.00 0.00
> MEMB
> ATOM 12821 0C21 POPE 388 4.740 56.570 63.940 1.00 0.00
> MEMB
> ATOM 12822 1H10 POPE 388 5.700 57.030 63.650 1.00 0.00
> MEMB
> ATOM 12823 1C21 POPE 388 4.030 55.900 62.790 1.00 0.00
> MEMB
> ATOM 12824 H11R OL 388 3.170 56.490 62.440 1.00 0.00
> MEMB
> ATOM 12825 H11S OL 388 3.610 54.920 63.130 1.00 0.00
> MEMB
> ATOM 12826 2C21 POPE 388 4.930 55.650 61.560 1.00 0.00
> MEMB
> ATOM 12827 H12R OL 388 5.010 54.560 61.410 1.00 0.00
> MEMB
> ATOM 12828 H12S OL 388 5.950 56.060 61.750 1.00 0.00
> MEMB
> ATOM 12829 3C21 POPE 388 4.430 56.280 60.260 1.00 0.00
> MEMB
> ATOM 12830 H13R OL 388 4.440 57.380 60.380 1.00 0.00
> MEMB
> ATOM 12831 H13S OL 388 3.380 55.970 60.090 1.00 0.00
> MEMB
> ATOM 12832 4C21 POPE 388 5.270 55.890 59.030 1.00 0.00
> MEMB
> ATOM 12833 H14R OL 388 5.200 54.790 58.880 1.00 0.00
> MEMB
> ATOM 12834 H14S OL 388 6.340 56.150 59.230 1.00 0.00
> MEMB
> ATOM 12835 5C21 POPE 388 4.830 56.620 57.760 1.00 0.00
> MEMB
> ATOM 12836 H15R OL 388 5.340 57.610 57.720 1.00 0.00
> MEMB
> ATOM 12837 H15S OL 388 3.740 56.810 57.830 1.00 0.00
> MEMB
> ATOM 12838 6C21 POPE 388 5.070 55.870 56.450 1.00 0.00
> MEMB
> ATOM 12839 H16R OL 388 4.580 54.870 56.510 1.00 0.00
> MEMB
> ATOM 12840 H16S OL 388 6.160 55.710 56.290 1.00 0.00
> MEMB
> ATOM 12841 7C21 POPE 388 4.460 56.620 55.250 1.00 0.00
> MEMB
> ATOM 12842 H17R OL 388 5.000 57.580 55.130 1.00 0.00
> MEMB
> ATOM 12843 H17S OL 388 3.400 56.860 55.500 1.00 0.00
> MEMB
> ATOM 12844 8C21 POPE 388 4.490 55.840 53.930 1.00 0.00
> MEMB
> ATOM 12845 H18R OL 388 5.520 55.550 53.660 1.00 0.00
> MEMB
> ATOM 12846 H18S OL 388 4.070 56.470 53.120 1.00 0.00
> MEMB
> ATOM 12847 H18T OL 388 3.880 54.920 54.010 1.00 0.00
> MEMB
> TER
>
>
>
> On 05/08/2012 02:28 PM, David A Case wrote:
> > On Tue, May 08, 2012, Albert wrote:
> >> charmmlipid2amber.x step5_assembly.pdb amber.pdb
> >>
> >>
> >> Currently supported lipids: DPPC DPPE DPPS DPPG DPPA
> >> DOPC DOPE DOPS DOPG DOPA
> >> POPC POPE POPS POPG POPA
> >> CHL1
> >>
> >> ERROR - No supported lipids found in pdb file.
> > The obvious question: do you indeed have some of the supported lipids
> in the
> > pdb file?
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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Received on Tue May 08 2012 - 10:00:04 PDT
