From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Aug 29 2012 - 13:47:31 CDT
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
>
>
>
>
>
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