Dear Amber users,
Lately,I have been trying to use amber to study the formation of an alternative conformation in a two domain protein. We have the structure of the two domains separately, which are linked by a long, disordered region, but we have cross-linking evidence on the interaction surface. Since we also know what the minimum and maximum distance is for the crosslinking reagents, my aim is to try to calculate the best possible solution to a complex which satisfies the crosslinking data. In order to do so, I originally thought to use distance restraints between the C-alphas of the cross-linked amino acids. The results have been far from optimal, though, as, rather then approximating the domains, only the corresponding amino-acids are approximated, with the secondary structure bing ripped apart.
Reading on the mailing list, I thought that EMAP restraints based on the starting coordinates for each of the domains might keep the domains compact. When I tried that, I didn't see any difference with the EMAP free simulation.
Does anybody have any ideas on how to do this?
Just in case, I'm posting my input and restraint files for you to check.
Thank you very much!
Manuel
Input file:
&cntrl
imin=0,irest=1,ntx=5,ioutfm=1, ntxo=2, nmropt=1
ntb=2,pres0=1.0,ntp=1,barostat=2
taup=2.0,
ntr=0,ntc=2,ntf=2,
tempi=300.0,temp0=300.0,ntt=3,ig=-1,gamma_ln=5
nstlim=1000000,dt=0.002,
ntpr=1000,ntwx=1000,ntwr=10000,
cut=8,iemap=1
/
&ewald
nfft1=64,nfft2=64,nfft3=64
/
&emap
mapfile='',
atmask=':1-91',
fcons=10, ifit=1,
move=1,
molfit='fit_Nt.pdb'
/
&emap
mapfile='',
atmask=':128-401',
fcons=10, ifit=1,
move=1,
molfit='fit_CT.pdb',
/
&wt type='DUMPFREQ', istep1=2 /
&wt type='END' /
DISANG=dist_pbc.RST
DUMPAVE=dist_pbc_vs_t
LISTIN=POUT
LISTOUT=POUT
END
Restraint file:
# bond restraints for pme
&rst iat= 935,5150, r1= 6, r2= 8, r3=11, r4=13, rk2=1.0, rk3=1.0, ir6=1, ialtd=0 /
&rst iat= 976,5150, r1= 6, r2= 8, r3=11, r4=13, rk2=1.0, rk3=1.0, ir6=1, ialtd=0 /
&rst iat= 330,5150, r1=9.4, r2=11.40, r3=27.40, r4=29.4, rk2=1.0, rk3=1.0, ir6=1, ialtd=0 /
&rst iat=1158,5150, r1=9.4, r2=11.40, r3=27.40, r4=29.4, rk2=1.0, rk3=1.0, ir6=1, ialtd=0 /
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Received on Thu Jan 08 2015 - 01:00:03 PST
