VMD-L Mailing List

From: Hélder Bandarra Tavares (H.D.BandarraTavares_at_tudelft.nl)
Date: Tue Jun 09 2020 - 09:35:48 CDT

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