> From: geyan <geyan.big.ac.cn>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Thu, 6 May 2010 08:39:45 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: Re: [AMBER] can't make proper use of IGB flag, it cause
> "inputconversion error"
>
> 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.
Not true...
Spores contain anywhere from 20-50% by weight water (compared to 80% water
for most cells), with an average density of 1.3 - 1.4g/mL.
See this article for the high diffusion of water in spores, but the proteins
are rotationally immobilized.
PNAS November 17, 2009 vol. 106 no. 46 19334-19339
I will leave it to the MD specialists on the list to determine the best
conditions to simulate the aqueous environment of a spore ;-)
Dean
>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,m
>> ynewly 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
>>
>> _______________________________________________
>> 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 Sat May 08 2010 - 17:30:03 PDT
