zhenwilliam
commented
1 year ago Dear Dr. @pstansfeld, Do you know what happened herein and how to fix this bug? Although I am not a computer science student, I am hopeful that this bug can be fixed to make this wonderful Colab Notebook more accessible to others.
I am eager to resolve this issue and was wondering if you could provide any insights on how to fix it. If it would be helpful, I would be happy to provide additional information or assist with troubleshooting.
Thank you for your help, and please let me know if there is anything else I can provide to assist.
Best regards, zhenwilliam
The error is entitled "FileNotFoundError: [Errno 2] No such file or directory: 'topol.top'"
The error happened in cell 6 and the who script was :
@title Set-up Coarse-Grained Membrane Protein System
%%capture os.chdir(working_dir)
for file in glob.glob(r'/content/martini*.itp'): print(file) shutil.copy(file, working_dir)
gromacs.make_ndx(f='memembed.pdb', o='index.ndx', input=('del 0', 'del 1-100','rDUM','q'),backup=False) gromacs.editconf(f='memembed.pdb',o='centered.pdb',n='index.ndx',c=True,d=3,input=(0,0),backup=False)
u = MDAnalysis.Universe('centered.pdb') x = round(u.dimensions[0]/10) y = round(u.dimensions[1]/10) z = round(u.dimensions[2]/10)
gromacs.confrms(f2='memembed.pdb', f1='centered.pdb', one=True, o='aligned.gro', input=(3,3),backup=False) gromacs.editconf(f='aligned.gro', o='protein.pdb',label='A',resnr=1,n=True,input=(0,0),backup=False)
v = MDAnalysis.Universe('aligned.gro') dum = v.select_atoms('resname DUM')
dm = (z/2) - (round(dum.center_of_mass()[2]/10))
with open('protein.pdb', 'r') as file : filedata = file.read() filedata = filedata.replace('HSE', 'HIS') filedata = filedata.replace('HSD', 'HIS') filedata = filedata.replace('MSE', 'MET') filedata = filedata.replace(' SE ', ' SD ') with open('protein.pdb', 'w') as file: file.write(filedata)
!martinize2 -f protein.pdb -dssp mkdssp -ff martini3001 -x protein-cg.pdb -o protein-cg.top -elastic -ef 500 -eu 1.0 -el 0.5 -ea 0 -ep 0 -merge A -maxwarn 100000 -scfix
!sed -e 's/^molecule./Protein 1/g' molecule.itp > protein-cg.itp
os.system('python2.7 /content/insane3.py ' + lipid + ' -salt 0.15 -sol W -o CG-system.gro -p topol.top -f protein-cg.pdb -center -x %s -y %s -z %s -dm %s' % (x, y, z, dm))
replacements = {'NA+':'NA', 'CL-':'CL', '#include "martini_v3.itp"':'#include "martini_v3.0.0.itp"\n#include "martini_v3.0.0_ions_v1.itp"\n#include "martini_v3.0.0_solvents_v1.itp"\n#include "martini_v3.0.0_phospholipids_v1.itp"\n'} lines = [] with open('topol.top') as infile: for line in infile: for src, target in replacements.items(): line = line.replace(src, target) lines.append(line) with open('topol.top', 'w') as outfile: for line in lines: outfile.write(line) with open('em.mdp','w') as em: em.write('integrator = steep\nnsteps = 5000\nemtol = 1000\nemstep = 0.001')
gromacs.grompp(f='em.mdp',o='em.tpr',c='CG-system.gro',maxwarn='-1',backup=False,v=True)
gromacs.mdrun(deffnm='em', c='CG-system.pdb',backup=False)
gromacs.trjconv(f='CG-system.pdb', o='CG-system.pdb', pbc='res', s='em.tpr', conect=True, input='0',backup=False)
%mkdir MD
gromacs.make_ndx(f='CG-system.pdb', o='index.ndx', input=('del 0', 'del 1-40', '0|rPOP*','1&!0','!1','del 1','name 1 Lipid','name 2 SOL_ION','q'),backup=False)
with open('cgmd.mdp','w') as md: md.write('integrator = md\ntinit = 0.0\ndt = 0.02\nnsteps = 10000\nnstxout = 0\nnstvout = 0\nnstfout = 0\nnstlog = 50000\nnstenergy = 50000\nnstxout-compressed = 50000\ncompressed-x-precision = 10000\nnstlist = 10\nns_type = grid\npbc = xyz\ncoulombtype = Reaction_field\nrcoulomb_switch = 0.0\nrcoulomb = 1.1\nepsilon_r = 15\nvdw_type = cutoff\nrvdw_switch = 0.9\nrvdw = 1.1\ncutoff-scheme = verlet\ncoulomb-modifier = Potential-shift\nvdw-modifier = Potential-shift\nepsilon_rf = 0\nverlet-buffer-tolerance = 0.005\ntcoupl = v-rescale\ntc-grps = PROTEIN LIPID SOL_ION\ntau_t = 1.0 1.0 1.0\nref_t = 310 310 310\nPcoupl = c-rescale\nPcoupltype = semiisotropic\ntau_p = 12.0\ncompressibility = 3e-4 3e-4\nref_p = 1.0 1.0\ngen_vel = yes\ngen_temp = 310\ngen_seed = -1\nconstraints = none\nconstraint_algorithm = Lincs\ncontinuation = no\nlincs_order = 4\nlincs_warnangle = 30\n')
gromacs.grompp(f='cgmd.mdp',o='MD/md',c='CG-system.pdb',maxwarn=-1, n='index.ndx',backup=False)