Re: Drude equilibration

From: Almeida-HernŠndez, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
Date: Mon Oct 05 2020 - 03:46:46 CDT

Solved by setting the missing:

temperature $temp

I guess those were bugs from CHARMM-GUI.

Bests

________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Almeida-HernŠndez, Yasser, Dr. <yasser.almeida-hernandez_at_uni-due.de>
Sent: Monday, October 5, 2020 10:35:52 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Re: Drude equilibration

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-HernŠndez, 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
Universitštsstr. 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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