Re: vmd-l: Re: Question regarding FEP parameters

From: Chris Harrison (charris5_at_gmail.com)
Date: Fri Aug 31 2012 - 20:06:54 CDT

Dear Snoze,

What is the actual error that is output with the crash? If no error,
send the last few lines of the log file.

It might be easiest if you also copy in your email your full config
file.

Best,
Chris

 

snoze pa <snoze.pa_at_gmail.com> writes:
> Date: Fri, 31 Aug 2012 12:06:48 -0500
> From: snoze pa <snoze.pa_at_gmail.com>
> To: namd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Re: namd-l: Question regarding FEP parameters
>
> Thanks Chris for your support.
>
> Somehow the system is working fine. However, if i try to increase the
> system temperature gradually, instead of keeping it FiX at 300, it crashes
> after going from temperature final cycle to Fep cycle.
>
> The heating is working fine, but the FEP crashes at line
>
> alch on
>
> However, if I remove the gradual heating, then everything is working fine.
> I am unable to figure out why?
>
> Here is my gradual heating code
>
> set temp 10;
> while { $temp <= 300 }
> {
> LangevinTemp $temp
> run 1000
> output Gradual_heating
> set temp [expr $temp + 10]
> }
>
>
> I think, based on FEP code that
>
> runFEPmin 0.0 0.0 0.0 $numSteps $numMinSteps $temp
>
>
> will read the $temp from above gradual final temperature.
>
>
> On Wed, Aug 29, 2012 at 3:32 PM, Chris Harrison <charris5_at_gmail.com> wrote:
>
> > snoze pa <snoze.pa_at_gmail.com> writes:
> > > Date: Wed, 29 Aug 2012 13:47:31 -0500
> > > From: snoze pa <snoze.pa_at_gmail.com>
> > > To: namd-l_at_ks.uiuc.edu, vmd-l_at_ks.uiuc.edu
> > > Subject: Re: namd-l: Question regarding FEP parameters
> > >
> > > To give you an idea about this error message I found following link
> > >
> > >
> > http://www.ncsu.edu/chemistry/franzen/public_html/CH795N/projects/GFP_MD.htm
> > >
> > > It says that:
> > >
> > > A common error arises from the fact that *Mutator* writes cross terms at
> > > the bottom of the psf file. to solve the problem delete those lines.
> > >
> > > If I delete those lines then it works fine.
> > >
> > > Do you think it is a right choice?
> > >
> > > Thanks
> > >
> > > On Wed, Aug 29, 2012 at 1:05 PM, snoze pa <snoze.pa_at_gmail.com> wrote:
> > >
> > > > Dear NAMD/VMD users,
> > > >
> > > > I am trying to prepare a molecule for FEP calculation. I am using vmd
> > to
> > > > prepare the psf file and namd for the simulation. Whole process is
> > smooth,
> > > > since the hybrid topology file is available in VMD directory. However,
> > when
> > > > I am running NAMD simulation, I am getting the error message.
> > > >
> > > > Reason: FATAL ERROR: UNABLE TO FIND CROSSTERM PARAMETERS FOR C NH1
> > CT1
> > > > C NH1 CT1 C NH1
> > > >
> > > > The error is obvious because the hybrid parameter file is missing. I
> > have
> > > > regular par_all22_prot.inp *parameter file* and *hybrid topology* file
> > > > top_all27_hybrid.inp. Mutation from Tyr to Ala is easy using* **hybrid
> > > > topology* file but to run the simulation I need *hybrid parameter*
> > file.
> > > > I already used the alchemify plugin in VMD to correct the psf file.
> > > >
> > > > However, using both psf file, I am getting the same error message.
> > > >
> > > > Does any one know where i can find the *hybrid parameter* file for all
> > > > amino acids used in FEP NAMD simulation.
> > > >
> > > > I will highly appreciate your help.
> > > >
> > > > Thank you,
> > > >
> > > > S
> > > >
> > > >
> > > >
> > > >
> > > >
> >
> > Snoze,
> >
> > This will work.
> >
> > In the future, please don't cross post on the namd and vmd lists the
> > same question. Thanks.'
> >
> > Best,
> > Chris
> >
> >
> > --
> > Chris Harrison, Ph.D.
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Theoretical and Computational Biophysics Group
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> >
> > http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
> > http://www.ks.uiuc.edu/~char Fax: 217-244-6078
> >
> >
> >

Best,
Chris

--
Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
http://www.ks.uiuc.edu/Research/namd       Voice: 773-570-6078
http://www.ks.uiuc.edu/~char               Fax:   217-244-6078

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