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
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue May 08 2012 - 07:00:02 PDT
