From: Almeida-Hernández, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
Date: Mon Oct 05 2020 - 03:35:52 CDT
I solved by setting set prot "segid dnaa .or. segid dnab" in step2_drude.str.
But now I get:
FATAL ERROR: Must have either an initial temperature or a velocity file
Any thoughts?
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Almeida-Hernández, Yasser, Dr. <yasser.almeida-hernandez_at_uni-due.de>
Sent: Monday, October 5, 2020 10:08:48 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Drude equilibration
Dear all,
I am trying to equilibrate a solvated DNA system with Drude FF, prepared with CHARMM-GUI, using NAMD 2.14b2 (Linux). I get this error when I run:
$ namd2 +p4 step4_equilibration.inp
(...)
TCL: wrong # args: should be "set varName ?newValue?"
FATAL ERROR: wrong # args: should be "set varName ?newValue?"
while executing
"set prot segid dnaa .or. segid dnab"
(file "../step2_drude.str" line 14)
invoked from within
"source ../step2_drude.str"
(file "step4_equilibration.inp" line 78)
FATAL ERROR: wrong # args: should be "set varName ?newValue?"
while executing
"set prot segid dnaa .or. segid dnab"
(file "../step2_drude.str" line 14)
invoked from within
"source ../step2_drude.str"
(file "step4_equilibration.inp" line 78)
[Partition 0][Node 0] End of program
Attached is my input file and the step2_drude.str file. What am I missing? I am relatively new to NAMD.
Thanks in advance.
-- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universitätsstr. 2, 45117 Essen Email: yasser.almeida-hernandez_at_uni-due.de<mailto:%20yasser.almeida-hernandez_at_uni-due.de> Phone: +49 201 183 2457<tel:+49%20201%20183%202457>
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