Dear David,
Thank you for your prompt reply.
Well, I have visually inspected the system by opening, with VMD, the topology and the md.nc file.
I will make a try with the command you suggested.
The strange parameter in the output is the super-stable (the same value) of the vdw.
I’ll get back to you ASAP.
Thanks in advance.
Vito
>
>
Vito Genna, Ph.D
EMBO Fellow
Scientist
Molecular Modelling and Bioinformatics
Orozco Lab
Dep. of Structural and Computational Biology
Institute for Research in Biomedicine (IRB Barcelona)
Parc Científic de Barcelona
C/ Baldiri Reixac 10-12
08028 Barcelona
P.S. Email written with my IPhone. Sorry for typo.
> Il giorno 10 ott 2018, alle ore 22:16, David A Case <david.case.rutgers.edu> ha scritto:
>
>> On Wed, Oct 10, 2018, Vito GENNA wrote:
>>
>> Once i got the system I minimize it and what I note is that water molecules
>> dramatically overlap protein's atoms.
>
> What is the evidence that this is happening? Did you visualize the
> system? Calculate the distance from a given water molecule to a given
> protein atom? Something else?
>
> You can use the "checkoverlap" command in cpptraj to print out all short
> contacts. There should be very few of these following minimization. It
> would probably also be more helpful to see the *output* from
> minimization, rather than the input file.
>
> Look carefully at the minimization and heating outputs for evidence of
> problems. It looks like you have 750 residues in your protein: is that
> correct? You might try a short calculation on a smaller fragment. I
> didn't notice anything wrong with your tleap input, but I could be
> missing something.
>
> ....dac
>
>
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Received on Wed Oct 10 2018 - 14:00:04 PDT
