Albert,
Did you try the latest script that I posted in the last email?
POPC should have three residues: PA, PC, and OL in that order.
POPE should have three residues as well: PA, PE, OL.
A PDB from CHARMM-GUI with those residues can be loaded ('loadpdb' command) into LEaP after you have loaded your force field (for example, 'source leaprc.lipid11').
Best,
Ben Madej
On May 8, 2012, at 11:58, "Albert" <mailmd2011.gmail.com> wrote:
> hello Ben:
> I've just got a question about the format of this script output. I
> found that my POPE molecule. As we can see from the following lines that
> one POPE was consist of different section including: POPE, OL,PA,PE and
> PC. Is that the correct Amber lipids11 FF format ?
>
> thank you very much
> best
> Albert
>
>
>
> TOM 6082 4C21 POPE 334 17.910 9.640 53.040 1.00 0.00 MEMB
> ATOM 6083 H14R OL 334 18.670 10.280 52.540 1.00 0.00 MEMB
> ATOM 6084 H14S OL 334 16.900 9.950 52.680 1.00 0.00 MEMB
> ATOM 6085 5C21 POPE 334 18.180 8.170 52.660 1.00 0.00 MEMB
> ATOM 6086 H15R OL 334 17.390 7.520 53.100 1.00 0.00 MEMB
> ATOM 6087 H15S OL 334 19.150 7.880 53.120 1.00 0.00 MEMB
> ATOM 6088 6C21 POPE 334 18.280 7.910 51.150 1.00 0.00 MEMB
> ATOM 6089 H16R OL 334 19.080 8.540 50.720 1.00 0.00 MEMB
> ATOM 6090 H16S OL 334 17.320 8.190 50.670 1.00 0.00 MEMB
> ATOM 6091 7C21 POPE 334 18.570 6.430 50.850 1.00 0.00 MEMB
> ATOM 6092 H17R OL 334 17.740 5.820 51.270 1.00 0.00 MEMB
> ATOM 6093 H17S OL 334 19.500 6.140 51.380 1.00 0.00 MEMB
> ATOM 6094 C118 OL 334 18.740 6.100 49.360 1.00 0.00 MEMB
> ATOM 6095 H18R OL 334 19.680 6.560 48.970 1.00 0.00 MEMB
> ATOM 6096 H18S OL 334 17.880 6.480 48.780 1.00 0.00 MEMB
> ATOM 6097 H18T OL 334 18.820 5.000 49.210 1.00 0.00 MEMB
> TOM 19873 H14S PA 110 -9.353 28.194 -1.421 1.00 0.00 MEMB
> ATOM 19874 C115 PA 110 -8.972 26.138 -1.757 1.00 0.00 MEMB
> ATOM 19875 H15R PA 110 -7.864 26.139 -1.683 1.00 0.00 MEMB
> ATOM 19876 H15S PA 110 -9.342 25.462 -2.557 1.00 0.00 MEMB
> ATOM 19877 C116 PA 110 -9.510 25.646 -0.400 1.00 0.00 MEMB
> ATOM 19878 H16R PA 110 -9.189 26.413 0.337 1.00 0.00 MEMB
> ATOM 19879 H16S PA 110 -9.007 24.673 -0.210 1.00 0.00 MEMB
> ATOM 19880 H16T PA 110 -10.617 25.571 -0.456 1.00 0.00 MEMB
> ATOM 19747 N31 PC 110 -12.022 39.831 -22.411 1.00 0.00 MEMB
> ATOM 19748 C32 PC 110 -11.408 40.988 -21.629 1.00 0.00 MEMB
> ATOM 19749 C33 PC 110 -11.703 38.471 -21.831 1.00 0.00 MEMB
> ATOM 19750 C34 PC 110 -13.518 40.084 -22.484 1.00 0.00 MEMB
> ATOM 19751 C35 PC 110 -11.518 39.718 -23.788 1.00 0.00 MEMB
> ATOM 19752 H2A PC 110 -11.640 41.924 -22.115 1.00 0.00 MEMB
> ATOM 19753 H2B PC 110 -10.334 40.888 -21.572 1.00 0.00 MEMB
> ATOM 19754 H3A PC 110 -12.341 37.716 -22.267 1.00 0.00 MEMB
> ATOM 19755 H3B PC 110 -10.658 38.287 -21.631 1.00 0.00 MEMB
> ATOM 19756 H3C PC 110 -12.166 38.309 -20.869 1.00 0.00 MEMB
> ATOM 19757 H4A PC 110 -14.134 39.353 -22.988 1.00 0.00 MEMB
> ATOM 19758 H4B PC 110 -13.989 40.359 -21.552 1.00 0.00 MEMB
> ATOM 19759 H4C PC 110 -13.611 40.885 -23.203 1.00 0.00 MEMB
>
> On 05/08/2012 08:36 PM, Benjamin D Madej wrote:
>> Hi Albert,
>>
>> Thanks for the bug report-- it was a problem with the ions from CHARMM. I have fixed the issue and updated the script to v1.1.1.
>>
>> All the best,
>> Ben
>> _____________
>
>
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Received on Tue May 08 2012 - 12:30:03 PDT
