Reply To: Missing common atom definitions in constraints

[Anonymous]

I think you’re right, that it’s using centroids, but I’m not totally sure. Here’s the script:

#!/bin/csh
#
# CS-ROSETTA: System for Chemical Shifts based protein structure prediction using ROSETTA
# (C) Shen and Bax 2007-2009, Lab of Chemical Physics, NIDDK, NIH
# Version 1.01(build 2009.1117.15)
#
# runRosetta3.com: performs a ROSETTA3.X structure generation
#

# set outDir = `cat paths.txt | awk ‘$1~”score”{print $2}’`

# set rand_1 = `( ps ax && netstat -a && date ) | sum | cut -c1-6`
# set rand_2 = `( ps ax && netstat -a && date ) | sum | cut -c1-2`
# set rand = {$rand_1}{$rand_2}

${rosetta3} -database ${rosetta3DB} -in::file::frag3 aat000_03.200_R3 -in::file::frag9 aat000_09.200_R3 -in::file::fasta t000_.fasta -in:fix_disulf disulf.cst -constraints:cst_fa_file TLL4_test_bound.cst -constraints:cst_fa_weight 10.0 -abinitio::use_filters false -nstruct 50 -increase_cycles 10 -rsd_wt_helix 0.5 -rsd_wt_loop 0.5 -rg_reweight 0.5 -abinitio::fastrelax -score::weights score13_env_hb -out::nstruct 50 -user_tag j003

Could I also just get it to run in fullatom mode to resolve this issue? If so, what’s the command for this? I am currently limited by available cpus, so I was hoping not to have to use fullatom in the fragment-based search. However, if that’s the only way to get it to read HA atoms, so be it.

Thank you for your help.