Re: [AMBER] 3D-RISM in amber20

From: David A Case <>
Date: Tue, 20 Jul 2021 21:21:09 -0400

On Tue, Jul 20, 2021, Priya Dey wrote:

>The following error is coming: *ERROR: a RESTART or TRAJ file is required*
>*In the amber20 manual, it is written the required inputs are "pdb file,
>prmtop file and xvv file". *

>So my query is (a) why is this error coming?

I don't know the answer to this one. I think a pdb file should be allowed,
provided that it was created by something like ambpdb, so that the order of
atoms is the same as in the prmtop file. But ambpdb requires a restart
or trajectory file, so requiring one of the latter is not supposed to be a big

>(b) If a restart file has to be used, which restart file should I use? (as
>I have tried with the initial restart file that is generated during system
>preparation: in that case the system is reading coordinates from the
>restart file whatever the pdb is given, and the output is similar for
>different pdbs.)

If you have done anything after the initial system prepartaion
(minimization, dynamics), you should have a restart file that corresponds to
the end of such a run. You need to choose a file that has the coordinates
you wish to use.

If you just have a generic PDB file (not coming from Amber) you will
probably need to feed that to tleap in order to obtain the desired restart

...hope this helps....dac

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Received on Tue Jul 20 2021 - 18:30:03 PDT
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