Thank You, i forget to introduce the force field for protein. Now i use protein.ff14SB. But now i have the error due to the Sodium atom. For this case, i used loadamberparams frcmod.ionsjc_tip3p. Again it shows the same error. I use the following commands in tleap
>source leaprc.gaff
>source leaprc.protein.ff14SB
>loadamberprep 1.prepin
>loadamberprep na.prepin
>loadamberparams 1.frc
>loadamberparams gaff.dat
>loadamberparams frcmod.ionsjc_tip3p
>abc = loadpdb 2.pdb
>addions abc Na +1
>source leaprc.water.tip3p
>solvatebox abc TIP3PBOX 10.0
>saveamberparm abc 1.top 1.crd
I got the error message as :
For atom: .R<Na+ 324>.A<Na 1> Could not find vdW (or other) parameters for type: Na
Thank You
with regards,
R. A. Jeyaram
________________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, September 12, 2017 4:51 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Atom does not have file type -reg.
On Mon, Sep 11, 2017, Jeyaram R A wrote:
>
>
> FATAL: Atom .R<ASN 22>.A<CA 2> does not have a type.
Did you load a protein force field? Look carefully at your tleap output.
One (often frustrating) feature/bug of tleap is that it will soldier
on even if there are errors. So (for example) if you misspelled the name
of the protein force field you want, tleap would print an error message,
but continue on, giving errors like that above.
Of course, there are other things that could have gone wrong, but the
output from tleap is pretty informative, once you get some experience in
reading it.
....dac
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Received on Tue Sep 12 2017 - 07:30:03 PDT
