spermine?

Discussions about the force fields implemented in Hippo. For general force field discussions see Molecular Simulations -> Force fields.
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kaihsu
Posts: 10
Joined: Wed Nov 12, 2008 3:23 pm
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spermine?

Post by kaihsu » Wed Nov 12, 2008 3:50 pm

What would the entry for spermine look like in hippo_protein_database.dat?

I have the following ligand and would like to perform a simulation with Hippo:
HETATM10361 N1 SPM E 1 -0.020 1.240 61.830 1.00 0.00 N
HETATM10362 HAA SPM E 1 -0.090 0.710 62.670 1.00 0.00 H
HETATM10363 HAB SPM E 1 0.850 1.740 61.830 1.00 0.00 H
HETATM10364 HAC SPM E 1 -0.780 1.900 61.800 1.00 0.00 H
HETATM10365 C2 SPM E 1 -0.090 0.340 60.660 1.00 0.00 C
HETATM10366 C3 SPM E 1 -0.020 1.040 59.290 1.00 0.00 C
HETATM10367 C4 SPM E 1 0.040 0.040 58.110 1.00 0.00 C
HETATM10368 N5 SPM E 1 0.070 0.670 56.770 1.00 0.00 N
HETATM10369 HAG SPM E 1 0.820 1.330 56.730 1.00 0.00 H
HETATM10370 HAH SPM E 1 -0.790 1.170 56.640 1.00 0.00 H
HETATM10371 C6 SPM E 1 0.220 -0.340 55.710 1.00 0.00 C
HETATM10372 C7 SPM E 1 0.220 0.270 54.290 1.00 0.00 C
HETATM10373 C8 SPM E 1 0.490 -0.770 53.180 1.00 0.00 C
HETATM10374 C9 SPM E 1 0.400 -0.160 51.770 1.00 0.00 C
HETATM10375 N10 SPM E 1 0.660 -1.140 50.700 1.00 0.00 N
HETATM10376 HAI SPM E 1 0.130 -1.970 50.860 1.00 0.00 H
HETATM10377 HAJ SPM E 1 1.630 -1.370 50.700 1.00 0.00 H
HETATM10378 C11 SPM E 1 0.280 -0.530 49.400 1.00 0.00 C
HETATM10379 C12 SPM E 1 0.350 -1.500 48.200 1.00 0.00 C
HETATM10380 C13 SPM E 1 0.000 -0.840 46.850 1.00 0.00 C
HETATM10381 N14 SPM E 1 0.110 -1.770 45.710 1.00 0.00 N
HETATM10382 HAE SPM E 1 1.060 -2.100 45.660 1.00 0.00 H
HETATM10383 HAF SPM E 1 -0.480 -2.560 45.850 1.00 0.00 H
HETATM10384 HAD SPM E 1 -0.130 -1.300 44.860 1.00 0.00 H

martin
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: spermine?

Post by martin » Wed Nov 12, 2008 7:00 pm

Ciao Kaihsu,

I've built is from opls-aa amine parameters, check out the updated forcefield and database files. I also attach the PDB it builds.

Please check that it's correct, (i also added the di-methyl-amine and di-ethyl-amine, from which i built it).

Have fun and let us know how you fare ;)
Best wishes,
Martin
Attachments
hippo_protein_database.dat
(150.67 KiB) Downloaded 492 times
oplsaa_forcefield.dat
(72.61 KiB) Downloaded 481 times
spermine.pdb
(3.42 KiB) Downloaded 457 times

kaihsu
Posts: 10
Joined: Wed Nov 12, 2008 3:23 pm
Contact:

Re: spermine?

Post by kaihsu » Thu Nov 13, 2008 11:53 am

Thanks! I will check.

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