tbereau / peptideb Goto Github PK

Hi Tristan,

I've been testing the examples with peptideB for some time. Everything works fine except for the remd. I use the command in the Wiki Page to run replica exchange as the fllowing
Espresso peptidebuilder.tcl polyala.tcl -replica -connect.
It returns

:: >  loaded version 1.0.0 of peptideb.
:: >  loaded version 1.0.0 of peptideb::input.
:: >  loaded version 1.0.0 of peptideb::espresso.
:: >  loaded version 1.0.0 of peptideb::output.
:: >  loaded version 1.0.0 of peptideb::utils.
:: >  loaded version 1.0.0 of mmsg.
:: >  
:: >  Replica exchange algorithm has been turned on.

and stops there all the time.
I followed closely the guides in the Installation Page, so I don't know what's wrong in the procedure. I tried other examples but it just stopped there.
I know it has been ten years since you worked on this project, so it would be great if you still remember something and give me some tips to get it run.

Thank you in advance,

Martin

Hi Tristan,

I followed the steps in the Wiki Installation, and tested the peptide.tcl file in examples folder:

peptidebuilder.tcl peptide.tcl
:: >
:: > ***********************
:: > * *
:: > * peptideB *
:: > * Tristan Bereau *
:: > * (2008) *
:: > * *
:: > ***********************
:: >
invalid command name "calc_lj_shift"
while executing
"calc_lj_shift $sigma $ljhp_cut"
("foreach" body line 17)
invoked from within
"foreach partner $3letter_list {
if {$partner != "GLY"} {
# The following condition will never be true because of the if statement two levels ab..."
("foreach" body line 28)
invoked from within
"foreach name $3letter_list {
# No interaction with GLY
if {$name != "GLY"} {
# The next line is there only in case we decide to turn on the nb
..."
(in namespace eval "::peptideb" script line 113)
invoked from within
"namespace eval peptideb {
variable bonded_parms ""
variable angle_parms ""
variable dihedral_parms ""
variable nb_interactions..."
(file "/homes/minhtien/Apps/peptideB/src/chain_interactions.tcl" line 17)
invoked from within
"source [file join [file dirname [info script]] chain_interactions.tcl]"
(file "/homes/minhtien/Apps/peptideB/src/chain_parameters.tcl" line 179)
invoked from within
"source /homes/minhtien/Apps/peptideB/src/chain_parameters.tcl"
("package ifneeded peptideb 1.0.0" script)
invoked from within
"package require peptideb"
invoked from within
"::mmsg::send $this "loaded version [package require peptideb] of peptideb.""
(file "/homes/minhtien/Apps/peptideB/peptidebuilder.tcl" line 33)

or with Espresso 3.3.1 on:

:: >
:: > ***********************
:: > * *
:: > * peptideB *
:: > * Tristan Bereau *
:: > * (2008) *
:: > * *
:: > ***********************
:: >
:: > loaded version 1.0.0 of peptideb.
:: > loaded version 1.0.0 of peptideb::input.
:: > loaded version 1.0.0 of peptideb::espresso.
:: > loaded version 1.0.0 of peptideb::output.
:: > loaded version 1.0.0 of peptideb::utils.
:: > loaded version 1.0.0 of mmsg.
:: >
::peptideb::utils > Setting the random seed to clock in seconds: 460554950
:: > Espresso integration is turned on.
:: > Langevin thermostat has been turned on.
::peptideb::input > Building peptide from file 'peptide.tcl'...
::peptideb::input > Configuration was parsed successfully.
:: > Chemical resolution was turned on.
::peptideb::espresso > Feeding peptide chain into ESPResSo...
::peptideb::espresso > The box size was set to: 40.0 40.0 40.0
::peptideb::espresso > Error: could not set interaction: 0 2 lj-angle 6.0 4.11 8. 1 -1 1 -2 2
excessive parameter/unknown interaction type "lj-angle" in parsing non bonded interaction

I also tried other example files and it reported same errors. It would be great if you can have a look at this case. I am really interested in your intermediate level of resolution CG model.

Thank you in advance,

Tien Phan

Hi Tristan,
When I attempted to run peptideB in Espresso 3.3.1, I received the following warning:
WARNING: "inter ljforcecap" is deprecated and will be removed in some further version. Use "inter forcecap" instead.

Would it be possible to update this to enhance compatibility especially since Espresso 3.4 has been released?

Hi Tristan,

I compiled the latest version of Espresso to run with peptideB. I noticed that the myconfig.h needed to have the #define MASS option in order to set individual masses, which in your current file is commented out by default.