Re: [AMBER] Water do not see the system....

From: Vito GENNA <>
Date: Wed, 10 Oct 2018 22:48:20 +0200

Dear David,

Thank you for your prompt reply.
Well, I have visually inspected the system by opening, with VMD, the topology and the 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 Genna, Ph.D
EMBO Fellow
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 <> 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
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