Usually people find an existing pdb to work from. Leap isn't
well-adapted to generating models from scratch. E.g. 'edit nterm' in
xleap to see how ugly the results of 'sequence' are, Leap doesn't have
the smarts to fold from scratch.
Bill
On 8/18/17 8:35 AM, RYDER WHITTAKER HAWKINS wrote:
> Hello,
>
> I am having a problem in the AmberTools LEAP command when it comes to imposing bond lengths.
> Here's the situation: I have the middle domain of my protein built with a homology model. I wish to add two random-coil peptides to the N- and C- termini in order to simulate the whole protein.
> My tleap.in reads like this:
> "
> source leaprc.protein.ff14SB
> source leaprc.DNA.OL15
> source leaprc.lipid17
> source leaprc.water.tip3p
> source leaprc.gaff2
> nterm = sequence { NMET ARG ASN PRO GLY GLY PRO GLY TRP ALA SER LYS ARG PRO LEU GLN LYS LYS GLN ASN THR ALA CYS LEU CYS ALA GLN GLN PRO ALA ARG HIS PHE VAL PRO ALA PRO PHE ASN SER SER ARG GLN GLY LYS ASN THR ALA GLN PRO THR GLU PRO SER LEU SER SER VAL ILE ALA PRO THR LEU PHE CYS ALA PHE LEU TYR LEU ALA CYS VAL THR ALA GLU LEU PRO GLU VAL SER ARG ARG MET ALA THR SER GLY VAL ARG SER LYS GLU GLY ARG ARG GLU HIS ALA PHE VAL PRO GLU PRO PHE THR GLY THR ASN LEU ALA PRO SER LEU TRP LEU HIS ARG PHE GLU VAL ILE ASP ASP LEU ASN HIS TRP ASP HIS ALA THR LYS LEU ARG PHE LEU LYS GLU SER LEU LYS GLY ASP ALA LEU ASP VAL TYR ASN GLY LEU SER SER GLN ALA GLN GLY ASP PHE SER PHE VAL LYS GLN ALA LEU LEU ARG ALA PHE GLY ALA PRO GLY GLU ALA PHE SER GLU PRO GLU GLU ILE LEU PHE ALA ASN SER MET GLY LYS GLY TYR TYR LEU LYS GLY LYS VAL GLY HIS VAL PRO }
> charge nterm
>
> cterm = sequence { LEU GLU ASP HIS ASN ALA VAL LEU ASP PHE GLU HIS ARG THR CYS THR LEU LYS GLY LYS LYS PHE ARG LEU LEU PRO VAL GLY SER SER LEU GLU ASP GLU PHE ASP LEU GLU LEU ILE GLU GLU GLU GLU GLY SER SER ALA PRO GLU GLY SER CHIS }
> charge cterm
>
> protease = loadpdb protease.pdb
> charge protease
>
> fullmodel = combine { nterm protease cterm }
> charge fullmodel
>
> bond nterm.204.C protease.1.N
> bond cterm.1.N protease.82.C
> savepdb fullmodel fullmodel.pdb
> quit
> "
>
> This all works fine (even with the long inputs), but the problem is the bond lengths are insanely long. In fact, so long that GROMACS cannot simulate them.
> I read the manual to see that the command to fix this is "impose" and so I tried to implement this in doing:
> "
> fullmodel = loadpdb fullmodel.pdb
> impose fullmodel { 204 205 } { { "C" "N" 1.32 } }
> quit
> "
> to get the right lengths for the peptide bonds. It didn't work. I got the error: "/Users/etudiants/Downloads/amber16/bin/tleap: line 10: 9154 Segmentation fault: 11 $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*"
>
> I also tried "impose fullmodel { 204 205 } { { "N" "C" 1.32 } }" and "impose fullmodel { { 1 999 } } { { "C" "N" 1.32 } }" with no luck.
>
> Anyone know how to solve this problem? It seems like it should be obvious.
> Maybe I should use the "sequence" command with my "protease" domain as an argument? like x = sequence { NMET HIS GLY THR protease THR SER SER CHIS }?
>
> Any hints would be appreciated. Note, I'm not a veteran linux coder or anything. I'm really just getting into this stuff.
> In case you're wondering my OS is "Darwin Kernel Version 15.6.0: Fri Feb 17 10:21:18 PST 2017; root:xnu-3248.60.11.4.1~1/RELEASE_X86_64 x86_64"
>
> Ryder Whittaker Hawkins
> MSc Candidate
> PI: Dr. Luc Vallières
> ryder.whittaker.crchudequebec.ulaval.ca
> ca.linkedin.com/in/ryderwh
> Work: (418) 525-4444
> Cell: (613) 979-7729
> Dept. of Molecular Medicine
> Université Laval (CHUL)
> 2705 Laurier Blvd
> Québec, QC
> G1V 4G2
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 18 2017 - 10:30:02 PDT
