On Fri, Feb 16, 2024, BILASH MAITY via AMBER wrote:
> I have prepared a system both in vacuum and solvated in water
> using amber force field in GLYCAM web builder. I am using the
> amber force field in NAMD 2.10 package to minimize the both
> system. In case of vacuum it is working properly, but in solvated
> system it is showing "Unexpected EOF in prmtop file". I have also
> tried the another versions of NAMD(2.10,2.12,2.5,2.8) to minimize
> the solvated system. But only the NAMD 2.5 version is working
> while others are showing the same error. I want to use the NAMD
> 2.10 version to minimize and equilibrate the solvated system.
>Can anyone predict the probable reason for this error, and suggest some way
>to figure this out.
Either NAMD help group or the GLYCAM people are probably better sources to
ask about this problem. Glycam uses (I believe) a somewhat unusual water
model (TIP5P), and NAMD might have problems with that.
I suspect it may be a pain, but running a minimization with sander would
help determine if the prmtop file is OK. (You can install AmberTools using
conda-forge, which is pretty straightforward.) But that still might not
explain why results depend on which version of NAMD you have.
...dac
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Received on Fri Feb 16 2024 - 11:00:03 PST
