Hi,
Thanks for your reply! Here is my answer to your question:
you haven't given enough information- how did you generate the initial
structure?
Here, I created the structure based on homology modeling. In fact it is a refined complex, from 10 ns MD (very stable for the wide type). When I obtained, this complex, I did a series of mutations on the complex . Then I try to use solvatecap to do 500 ps MD to refine every complexes (mutants).
how did you do the equilibration?
Firstly, I minimize the water, then minimize the whole system;
Secondly, I used 20 ps increase T from 0 to 300; then equilibrate it using 30 ps.
Thirdly, it is the production stage attached below.
are all of the force field parameters standard, or did you create any new ones?
I think it should be standard, as I obtained these parameter based the tutorial. But I am still not so confident.
what are you restraining?
I restrain residues (of the receptor) outside the binding site (with a radius of 6).
Can you give me more suggestions? I found using solvatecap can really amazing some time, but also sometime it makes the system change too drastical. I can hardly believe it.
Best regards,
Rilei Yu
--- 10年5月4日，周二, Carlos Simmerling <carlos.simmerling.gmail.com> 写道：
发件人: Carlos Simmerling <carlos.simmerling.gmail.com>
主题: Re: [AMBER] molecular dynamics set up
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年5月4日,周二,上午7:57
you haven't given enough information- how did you generate the initial
structure? how did you do the equilibration? are all of the force field
parameters standard, or did you create any new ones? what are you
restraining?
>
>
>
> Dear AMBER users,
>
> Recently, I tried to using solvatecap to simulate my system for faster
> speed. Unfortunately, sometime the ligands change drastically, even the
> ligand goes out the binding site in some simulation.
>
> I try to solve this problem using all kinds of ways:
> extending the cap radius;
> using smaller steps(0.001);
> adding some restraint;
> slowly increasing T;
> Unfortunately, the system is still not very stable as I expected. Here, I
> give the simulation file as follows and really hope anyone can give me some
> suggestions:
> #ntx=5,
> irest=1,
> imin=0,
> ntpr=1000,
> ntwx=1000,
> ntwr=5000,
> nstlim=250000,
> dt=0.001,
> ntt=3,
> gamma_ln = 1.0,
> temp0=300,
> tempi=300,
> tautp=1,
> igb=0,
> ntb=0,
>
> ntf=2,
> ntc=2,
> cut=15,
> ntr=1,
> fcap=2.5,
> ivcap=0,
> tol=0.000001,
> ntr=1, restraint_wt=5.0, restraintmask=':1-92, 95-144, 153-185, 200-243,
> 251-266, 273-288, 292-320, 324-326, 332-372, 375-377, 382-419',
> #I am really appreciated for your help!
>
> Rilei Yu
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 03 2010 - 18:00:03 PDT
