Dear Amberist
Good morning...
I have a novel peptide and is incorporated with non standard amino acid
residues. I have already cracked all the possible steps to handle it in
AMBER and now I have obtained preliminary structure with the NOE violation
of 0.2-0.7 A* (200 noes + 20 hydrogen bonds). But my system visually looks
70% close to the expected structure but I would like to improve it.
Currently I have annealed my system with noe, hydrogen bond restraints in
vacuum.
My questions are...
1) What are next steps that I have to take to further improve its quality
of my system preliminary structure from SANDER (with RST-noe&hb) .
Unfortunately, my sample is not labelled and quality of 2D NOESY spectra is
good but I cant play bit more to obtain additional restraints. I don't have
RDC, I cant have Dihedral for this nonstandard part. So, could any one
suggest me steps one must follow after annealing with RST in vacuum.? In
addition, side chains with + and - charge are close. Even after using the
15A* cutoff.
2) Is it possible to perform annealing in TIP3BOX. I have tried but sander
blowup the system. If any one have good scripts for this could I request
them? I have tried in GB but my structure didn't improve. I just used the
GB annealing scripts on the same vacuum prmtop, .rst files.
3) I also have Zn coordination in my peptide. For annealing in vacuum I
have prepared my prmtop and inpcrd file with charge (to neutralize system)
and bonds between 2CYS and 2HIS. If I have to perform annealing or MD
TIP3BOX, could I directly use low energy structure (from annealing with
RST) as a input pdb to generate solvate.prmtop and solvate.inpcrd.
I would be very grateful for your help, suggestions...
thanks in advance
Vince
PS : annealing script that I am currently using is (below). In case how to
change these script to TIP3BOX annealing.
simulated annealing protocol, 20 ps
&cntrl
nstlim=20000, pencut=-0.001, nmropt=1, tempi=20m temp0=20
ntpr=200, ntt=1, ntwx=200,
cut=15, ntb=0, vlimit=10,
/
&ewald
eedmeth=5,
/
#
#Simple simulated annealing
algorithm:
#
#from steps 0 to 5000: heat the system to 600K
#from steps 5001-18000: re-cool to low temperatures with long tautp
#from steps 18001-20000: final cooling with short tautp
#
&wt type='TEMP0', istep1=0,istep2=5000,value1=600.,
value2=600., /
&wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
value2=100.0, /
&wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
value2=0.0, /
&wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
value2=0.4, /
&wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
value2=4.0, /
&wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
value2=1.0, /
&wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
value2=0.05, /
&wt type='REST',
istep1=0,istep2=3000,value1=0.1,
value2=1.0, /
&wt type='REST',
istep1=3001,istep2=20000,value1=1.0,
value2=1.0, /
&wt type='END' /
LISTOUT=POUT
DISANG=RST_noe&hb
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Received on Fri Oct 23 2015 - 02:30:05 PDT
