+ if instance.type == 'dock' and instance.md_seq2 != '':
+ with open(instance.jobdirname+'/file2.inp','w') as f:
+ f.write(instance.name + ' chain2 random start'+ '\n')
+ control_line = 'SEED='+str(instance.md_seed)+' '\
+ +'rand_conf md one_letter'\
+ + ' BOXX=1000 BOXY=1000 BOXZ=1000 '
+
+ if instance.unres_ff =='NEWCT-9P':
+ control_line = control_line+'tormode=2 cart'
+
+ type_line = ' reset_vel=0'\
+ +' t_bath=300'\
+ +' nstep=100000'\
+ +' ntwe=10000'\
+ +' ntwx=100000'\
+ +' dt=0.2 lang=1 scal_fric=0.02 respa mdpdb '
+
+ wrapper = textwrap.TextWrapper(width=70)
+ word_list = wrapper.wrap(text=control_line)
+ for element in word_list[:-1]:
+ f.write('{:79}'.format(element)+'&\n')
+ f.write(word_list[-1]+'\n')
+
+ word_list = wrapper.wrap(text=type_line)
+ for element in word_list[:-1]:
+ f.write('{:79}'.format(element)+'&\n')
+ f.write(word_list[-1]+'\n')
+
+ f.write(w+'\n')
+
+ seq=instance.md_seq2.replace(" ","")
+ f.write(str(len(seq))+'\n')
+ for i in range(0,len(seq),80):
+ f.write(seq[i:i+80]+'\n')
+ f.write('0\n')
+ f.write('0\n')
+
+