Dear Amber Users,
I am a fairly new user of amber tools, and so far it was going great. I have, however, run into some problems.
I can construct my carbohydrate molecule in sleap, that's fine. I would like to actually end up with multiple instances of that molecule for my simulation, neatly packed in a very precise way, and for that I have used packmol. In packmol I arrange the molecules plus water and some ions, and I end up with a .pdb file with everything in it.
I then proceed to use that file in sleap again, in order to create coordinate and parameter files. That's were things go wrong...and I end up with a wrong topology file. Also, when I save the same .pdb file through leap, it ends up a bit messy..
So basically, the first time sleap works great, and the second time not so much...This doesn't surprise me, really, but I still have no idea how to fix it. I don't get any errors or problems using sleap by the way, both the first and second time.
At the end of this msg I have posted the first and second inputs for sleap. The first is more or less directly taken from the Glycam website and features some minor changes, but it works great to create a single molecule.
Also, if someone thinks I'm going about this completely the wrong way, do let me know. Apologies if this is too basic !
Maria
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Input 1:
source leaprc.ff99SB
source leaprc.Glycam_06
loadamberprep N-ASN.prep
# This is an asparagine-linked oligosaccharide
set GNN tail GNN.1.ND2
amber_seq = sequence { GNN 4YB 4YB VMB }
set amber_seq tail amber_seq.4.O6
amber_seq=sequence { amber_seq VMA }
set amber_seq tail amber_seq.5.O6
amber_seq=sequence { amber_seq 0MA }
set amber_seq tail amber_seq.5.O3
amber_seq=sequence { amber_seq 0MA }
set amber_seq tail amber_seq.4.O3
amber_seq=sequence { amber_seq 2MA 0MA }
impose amber_seq {3 2} { {H1 C1 O4 C4 60.0} }
impose amber_seq {3 2} { {C1 O4 C4 H4 0.0} }
impose amber_seq {4 3} { {H1 C1 O4 C4 60.0} }
impose amber_seq {4 3} { {C1 O4 C4 H4 0.0} }
impose amber_seq {5 4} { {H1 C1 O6 C6 -60.0} }
impose amber_seq {5 4} { {O6 C6 C5 O5 60.0} }
impose amber_seq {5 4} { {C1 O6 C6 C5 180.0} }
impose amber_seq {8 4} { {H1 C1 O3 C3 -60.0} }
impose amber_seq {8 4} { {C1 O3 C3 H3 0.0} }
impose amber_seq {6 5} { {H1 C1 O6 C6 -60.0} }
impose amber_seq {6 5} { {O6 C6 C5 O5 60.0} }
impose amber_seq {6 5} { {C1 O6 C6 C5 180.0} }
impose amber_seq {7 5} { {H1 C1 O3 C3 -60.0} }
impose amber_seq {7 5} { {C1 O3 C3 H3 0.0} }
impose amber_seq {9 8} { {H1 C1 O2 C2 -60.0} }
impose amber_seq {9 8} { {C1 O2 C2 H2 0.0} }
charge amber_seq
check amber_seq
saveamberparm amber_seq prmTop.top prmCoord.crd
savepdb amber_seq prm.pdb
(then I use packmol to end up with the new packed_molecules.pdb)
Input 2:
source leaprc.ff99SB
source leaprc.Glycam_06
loadamberprep N-ASN.prep
set GNN tail GNN.1.ND2
new_array = loadPdb packed_molecules.pdb
charge new_array
saveamberparm new_array array.top array.crd
savepdb new_array array.pdb
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Received on Fri Jan 28 2011 - 10:00:04 PST
