On Tue, Aug 20, 2013 at 12:16 PM, egeh00 <egeh00.aol.com> wrote:
> Dear Ross,
>
> Thank you for your relply. I made the prmtop and inpcrd file with tleap in
> ambertools1.5. And I did not find the item you shown to me in my promtop
> files. Also, in the mdout files, it shows that sander did not find the
> factor in topology files, so sander used the default value. Is that caused
> by my low version ambertools or tleap?
Yes. tleap did not start writing variable 1-4 scaling information to the
topology file until the 3rd update in AmberTools 1.5 (I presume the version
on the machine you are using is unpatched). You can either update to the
latest version of AmberTools or request that your HPC staff upgrade
AmberTools 1.5 with all of the current bug fixes. (I would personally
suggest upgrading to AmberTools 13)
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 20 2013 - 09:00:02 PDT
