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Thu, 11/28/2013 - 11:29 — losadminos
Forums: 
Usage

Multichain protein modeling

Wed, 03/27/2013 - 11:54 — PengJH

Dear Developers,

I was modeling hfq hexamer using UNRES, position restraints were imposed within each chain.
The hexamer disassembled at last, and I could not figure out what was going wrong with the input.
The structure model was from pdb 1HK9 and C terminals of each chain were built from homology modeling.

The input file is like following:

hfq-pr
SEED=-3059743 pdbstart pdbref refstr rescale_mode=2 md sym=6 &
CONSTR_DIST=3 pdbout
nstep=100000 ntwe=1000 ntwx=1000 dt=0.01000 lang=0 t_bath=300 damax=1000 tbf &
restart rest mdpdb reset_moment=1000 reset_vel=0 DISTCHAINMAX=60
WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
WVDWPP=0.11371 WHPB=1.00000 &
CUTOFF=7.00000 WCORR4=0.00000
hfq.pdb
0
0
nfrag=6 ifrag=2 103 105 206 208 309 311 412 414 515 517 618 &
wfrag=100 100 100 100 100 100 DIST_CUT=7.0

 

Sat, 03/30/2013 - 07:33 — adam.liwo

Re: Multichain protein modeling

Hi Peng,

It would help if you could send me (to adam@chem.univ.gda.pl) a stat file from MREMD or post excerpts from it on the forum. I'd suspect that the initial structure was too strained and this is why the hexamer blew up into pieces but without having a look into the simulations. Anyway, I'd suggest to carry a short simulation with imposing restraints on WHOLE hexamer structure, including the distances between monomers and then, after it relaxes, remove the restraints on the distances betweeen monomers. In this initial short simulation (100,000 - 200,000 MREMD steps), you might want to use a shorter time step, dt=0.01 or 0.02 or even shorter, depending on how the simulation behaves.

Adam

 

Mon, 04/15/2013 - 10:11 — PengJH

Dear Professor Adam, Thank

Dear Professor Adam,
Thank you very much for your advice. It's right about the too strained initial structure. After imposing restraints on WHOLE hexamer, I ran a short simulation with small time step dt=0.01 for 100,000 steps removing restraints on the distances between monomers, and then a normal time step of dt=0.1.

But when I am trying to model another complex mimicking this way with a time step of even , energy of the protein complex did not drop during the short simulation with restraints on WHOLE complex.
Simulation was terminated after 63,000 steps.
The last line of the stat file is like this:
63000 4.74 64809.240************************ 0.81 0.693 0.248 0.043 0.000 9293.194 300.000 35.358 0
And following sentence is in the end of *.out_GB file:
***************** Elapsed time ( 55800.33 s) is within the safety limit ( 1800.00 s) of the allocated time ( 57600.00 s). Terminating.

Is this caused by a bad initial structure? And if so, how could I improve the quality of the initial structure?

Thanks a lot for your patience, dear Professor.
Best Wishes,
Peng

Following is the inp file
SEED=-3059743 pdbstart pdbref refstr rescale_mode=2 md CONSTR_DIST=3
nstep=100000 ntwe=1000 ntwx=1000 dt=0.0001 lang=0 t_bath=300 damax=1000 &
dvmax=2000 edriftmax=1000 mdpdb restart rest tau_bath=1.0 reset_moment=1000 &
reset_vel=0 tbf
WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
WVDWPP=0.11371 WHPB=1.00000 &
CUTOFF=7.00000 WCORR4=0.00000
cvn.pdb
0
0
nfrag=2 ifrag=2 1065 1067 1205 wfrag=100 100 DIST_CUT=7.0

 

Mon, 04/15/2013 - 19:19 — adam.liwo

Hi Peng, Thank you for

Hi Peng,

Thank you for feedback.

Please try minimization first. Instead of the following first lines of input

SEED=-3059743 pdbstart pdbref refstr rescale_mode=2 md CONSTR_DIST=3
nstep=100000 ntwe=1000 ntwx=1000 dt=0.0001 lang=0 t_bath=300 damax=1000 &
dvmax=2000 edriftmax=1000 mdpdb restart rest tau_bath=1.0 reset_moment=1000 &
reset_vel=0 tbf

you say

SEED=-3059743 pdbstart pdbref refstr pdbout rescale_mode=2 minimize &
CONSTR_DIST=3
mafun=5000

(remember to put the "&" in the 80th column)

If minimization is successful, it will ouypuy the minimized conformation in the PDB file in UNRES format. Then you start from this pdb file instead of the experimental pdb file:

SEED=-3059743 pdbstart pdbref refstr unres_pdb rescale_mode=2 md CONSTR_DIST=3
nstep=100000 ntwe=1000 ntwx=1000 dt=0.0001 lang=0 t_bath=300 damax=1000 &
dvmax=2000 edriftmax=1000 mdpdb restart rest tau_bath=1.0 reset_moment=1000 &
reset_vel=0 tbf
WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
WVDWPP=0.11371 WHPB=1.00000 &
CUTOFF=7.00000 WCORR4=0.00000
pdb_from_UNRES.pdb
0
0
nfrag=2 ifrag=2 1065 1067 1205 wfrag=100 100 DIST_CUT=7.0

The unres_pdb keyword is required to tell the program that the input pdb file is the UNRES pdb file.

 

Tue, 04/16/2013 - 13:04 — PengJH

Dear Professor Adam, I've

Dear Professor Adam,

I've tried energy minimization of the complex using the parameters given above, and the minimization failed, the screen output reads:

Call Read_Bridge.
after etotal
Calling OVERLAP_SC
SC_move 0 NaN
Calling MINIMIZE.
SUMSL return code is 3 eval 2
# eval/s 1.05795023252283
refstr= T
CG processor 0 is finishing work.
Bye Bye...

and Total wall clock time 7.21949696540833 sec

Is it caused by the unusual etot? I just cannot figure out where I am going wrong.

Best Wishes!
Peng

 

Tue, 04/16/2013 - 21:08 — adam.liwo

Re: minimization

Hi Peng,

I think the published version must have problems with minimization. We'll be publisning the next release in which we fixed the problems in the end of the week; for now, I'll send you the current best minimization version.

Best regards,

Adam

UNited RESidue model of proteins (UNRES)