VMD-L Mailing List

From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Tue Jun 09 2020 - 22:14:48 CDT

Hi Hélder,

I re-ran 50,000 steps of simulation of an insulin structure using the exact
TkConsole commands you linked there, and I did not have the same fatal
error in namd. Are you certain the error comes from your fixing of the
atoms? The process you're following for fixing your atoms seems to be a
very common one for fixing atoms - but if it's failing, have you considered
using restrained atoms (constraint keyword,
http://www.ks.uiuc.edu/Research/namd/2.13/ug/node27.html) instead of Fixed
atoms? Constraints seem less likely to cause fatal errors than restraints.

Kind regards,
Michael Robinson

On Wed, 10 Jun 2020 at 02:10, Hélder Bandarra Tavares <
H.D.BandarraTavares_at_tudelft.nl> wrote:

> Hello everyone,
>
>
> I'm trying to do a minimization/equilibration with NAMD keeping certain
> atoms fixed. However, after it runs for a while, I get this message: "FATAL
> ERROR: Exiting prematurely; see error messages above.". Worth noting that
> it doesn't actually display any messages above.
>
>
> My input file contains the following:
>
>
> "fixedAtoms on
> fixedAtomsFile fixedatoms.pdb
> fixedAtomsCol B"
>
> and my fixedatoms.pdb file looks like this (this isn't the whole file, it
> goes on):
>
>
> "CRYST1 99.502 103.306 107.850 90.00 90.00 90.00 P 1 1
> ATOM 1 N ALA P 1 -18.049 -10.126 38.808 1.00 1.00
> PROA
> ATOM 2 HT1 ALA P 1 -18.738 -10.869 39.040 1.00 1.00
> PROA
> ATOM 3 HT2 ALA P 1 -17.358 -10.496 38.124 1.00 1.00
> PROA
> ATOM 4 HT3 ALA P 1 -18.544 -9.311 38.394 1.00 1.00
> PROA
> ATOM 5 CA ALA P 1 -17.359 -9.710 40.016 1.00 1.00
> PROA
> ATOM 6 HA ALA P 1 -16.706 -10.502 40.350 1.00 1.00
> PROA
> ATOM 7 CB ALA P 1 -16.558 -8.434 39.568 1.00 1.00
> PROA"
>
> With the value closer to "PROA" varying according to whether I want the
> atom to be fixed or not. This file was generated doing something similar to
> this:
>
> "set all [atomselect top all]
> set fixatom [atomselect top "protein"]
> $all set beta 0
> $fixatom set beta 1
> $all writepdb fixprotein.pdb"
>
> As it seems to me that I've done everything as I read in tutorials and in
> other messages I found, I'm having some trouble identifying the problem
> that's preventing the simulation from running, and would really appreciate
> if someone could help me on this.
>
> Best regards,
> Hélder Tavares
>
>