From: snoze pa (snoze.pa_at_gmail.com)
Date: Fri Aug 31 2012 - 12:06:48 CDT
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
>
>
>
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