I'm very sorry,I made a big mistake by saying implicit solvent to explicit solvent.What I meant to do is to simulate the interaction of my DNA and protein complex in spores,that clearly has no water.But with the helpful suggestions of others here,I decide to do the MD in implicit solvent effect and meet the problems I have issued.
Sorry to confuse you.Thanks for your help.
2010-05-06
geyan
发件人： Carlos Simmerling
发送时间： 2010-05-06 19:18:45
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] can't make proper use of IGB flag, it cause "inputconversion error"
I'm much more worried by what you are trying to do than the error messages
you are getting. combining GB with an explicitly solvated system is, in my
opinion, a bad idea unless you know exactly what you are doing.
I'm not sure what you mean by some of your statements.
why "out of necessity"? for a large system, GB is probably much slower per
step than using PBC and PME. by using GB and explicit water, you are getting
the inaccuracy and slowness of GB along with the viscoty of explicit water-
the worst features of both and probably no benefit. I emphatically recommend
against this.
when you say that you tested igb=1 and "it's OK", what tests did you run? we
have shown in published work that igb=1 combined with explicit water
performs very badly- the problem is that the solvation energy of the
explicit water in igb=1 is very far from correct. once again, I recommend
against this, and if I reviewed a manuscript that used this combination I
would probably recommend against publication.
so although you might be able to get these inputs to work, my advice is to
think about whether this really gives you a benefit, and do some careful
comparisons. this would not mean short MD showing that the system doesn't
fall apart, but something that relly tests the accuracy. also do timing
comparisons to make sure that this is actually faster than the methods
nearly everyone else uses (its hard to imagine that it would be, since you
should not be using a cutoff with GB and that will be very slow).
On Thu, May 6, 2010 at 4:30 AM, geyan <geyan.big.ac.cn> wrote:
> Hello all Amber users and Ross,
> Out of necessity,I have to do a MD under explicit solvent by turning on
> the IGB flag. I have tested the case of the Amber Basic tutorial with
> explicit solvent
> by setting IGB=1 and it's OK.In my system,a complex composed of DNA and
> proteins,I do MD by following the steps,first minimization,then heating
> stage,
> then density stage,then equilibration stage,at last,the production
> stage.But if I turn on the IGB,the MD will crash with the calculating
> extending.
> >From the error file produced,I got the following message:forrtl: severe
> (64): input conversion error, unit 9, file
> /home_soft/home/wujy/geyan/Amber/ABC_com_implicit/com_md5.rst
> Then I searched the archive of Amber,and found Ross has discussed with
> others about this issue,
> http://structbio.vanderbilt.edu/archives/amber-archive/2006/2736.php.Truely,mynewly produced .rst file has **** in it.But now the question is by simply
> following her instructions,that is changing the ntx=6 won't work because it
> will bring the error like this: forrtl: severe (39): error during read, unit
> 9, file
> /home_soft/home/wujy/geyan/Amber/ABC_com_implicit/density.rst.Regarding the
> NTXO,as far as I know,the default value in Amber10 is 1.
> So how to figure out this problem? I am very confused that if I don't
> turn on the IGB flag,and make other parameters the same as before,the whole
> process of MD will work well.
>
> The details of my input is in attach.
>
> Any suggestion is appreciated.
>
>
>
> --------------
> geyan
> 2010-05-06
>
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Received on Thu May 06 2010 - 07:00:05 PDT
