[ESPResSo-users] Setting Up protein aggregation simulation

[Olujide Olubiyi]

Dear users,

I'm new to Espresso and I encountered the following error message while trying 
to run the input script(attached below):

    ::peptideb::espresso > Error:  could not set interaction: 0 2 lj-angle 6.0 
4.11 8. 1 -1 1 -2
    excessive parameter/unknown interaction type "lj-angle" in parsing non 
bonded interaction

I tried uncommenting the appropriate sections of the myconfig.h file. A 
snapshot of this is:

define TABULATED
define LENNARD_JONES
define SMOOTH_STEP
/* define BMHTF_NACL */
/* define LJ_WARN_WHEN_CLOSE */
/* define MORSE */
 define LJCOS
/* define LJCOS2 */
define LJ_ANGLE
define LENNARD_JONES_GENERIC
 define BUCKINGHAM
/* define SOFT_SPHERE */
/* define INTER_DPD */
/* define INTER_RF */

/* Note: Activate ONLY ONE bonded 
define BOND_ANGLE_HARMONIC
 define BOND_ANGLE_COSINE
/* #define BOND_ANGLE_COSSQUARE */

I'm sure there are lot of things I'm likely to have done wrong, I will be 
grateful if anyone could point this out to me. I 
used the command:

Espresso peptidebuilder.tcl gnnqqny_15june_1.tcl -espresso

And here is the content of the configuration file:

set amino_acids {
    {GLY ASN ASN GLN GLN ASN TYR}
    {GLY ASN ASN GLN GLN ASN TYR}
    {GLY ASN ASN GLN GLN ASN TYR}
    {GLY ASN ASN GLN GLN ASN TYR}
    {GLY ASN ASN GLN GLN ASN TYR}
    {GLY ASN ASN GLN GLN ASN TYR}
}

set display_O_H "on"

set directory "gnnqqny_15june_1"
set PDB_file "$directory"
set filenumber 0

set espresso_switch "on"

set setbox_l {49.5 49.5 49.5}

set warm_time_step 0.01
set main_time_step 0.01
set verlet_skin 0.4
set langevin_gamma 1.0
set systemtemp [expr 1.*$eps]
set charges "off"
set warm_steps 50
set warm_n_times 20
set int_steps 1000
set int_n_times 50000
set pdb_freq 10

# Set the replica exchange temperatures
# 200 239 286 342 409 489 585 700 K
#set replica_temps { 0.67 0.80 1.00 1.15 1.37 1.64 1.96 2.35 }

#200 217 233 250 267 283 300
set replica_temps { 0.63 0.68 0.73 0.78 0.82 0.86 0.89 0.91 0.93 0.95 0.98 1.01 
1.06 1.12 1.17 1.22 }

# number of times to integrate between each replica MC step
set replica_timestep 1000
# number of replica exchange rounds
set replica_rounds 500000
# frequency at which replica pdb files are written
set replica_pdb_freq 10

Best regards,
Jide Olu
German Research School for Simulation Sciences,
Germany.