Re: [ESPResSo-users] Setting Up protein aggregation simulation

[Tristan Bereau]

Hi,

Did you recompile Espresso after uncommenting the LJ_ANGLE feature in
the myconfig.h file? It seems like that feature is not installed.

Best,
Tristan

On Mon, Jul 25, 2011 at 3:33 PM, Olujide Olubiyi <address@hidden> wrote:
> 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.
>
>