VMD-L Mailing List

From: Hélder Bandarra Tavares (H.D.BandarraTavares_at_tudelft.nl)
Date: Wed Jun 10 2020 - 05:55:09 CDT

Hi Michael,

Thank you very much for your response. I'm not sure the error comes from fixing the atoms, but it has not happened under any other circumstances so I'd assume that's the case.
Thank you for the suggestion, I will try doing it with constraints.

Kind regards,
Hélder Tavares
________________________________
From: Michael Robinson <michael.robinson1_at_monash.edu>
Sent: 10 June 2020 05:14:48
To: Hélder Bandarra Tavares
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Fixed atoms

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=yJwzsO_GDNn4u-K3xxj662nnwFBzY1fitnqTAVFTHQw&s=9YxQgQbOVATVCGXNXHLwvVq_NYekHhKlzn_lgm8NBNQ&e=>) 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<mailto: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