Enter the pdb name (name before underscore) : wt
Enter the name of the first element of the system : l
Enter the name of the second element of the system : z
Enter the name of the topology file (it must be put in lib directory) [default top_all22_prot.inp] : top_all27_prot_lipid.inp
Enter the name of the parameter file (it must be put in lib directory) [default par_all22_prot.inp] : torben_prot27_lipid32.prm
Enter skip used during your dynamic simulation : 1
Number of restarts of the dynamics : 1
Number of coordinate sets in cor file : 8002
Number of conformations needed : 25
Enter the number of chain : 2
Enter the name of chains in the order of appearance in the basic psf separated by a comma : l,z
Enter 1,2,3 or 4 according to the case: 2
        1 if your ligand is form by only one compound
        2 if your ligand is a whole chain
        3 if your ligand is only a part of chain
        4 other
Enter the number of residue of the compound (in the original crd for case 1) :
Enter the name of the compound (in the original crd for case 1) :
Enter the name of the chain of the ligand (for case 2 and 3) : z
Enter the number of the first residue of the ligand (in the original crd for case 3) :
Enter the number of the last residue of the ligand (in the original crd for case 3) :
Enter the definition with charmm keyword of the first part with bracket :(segid l)
Enter the definition with charmm keyword of the second part with bracket :(segid z)
###### For elec calculation using UHBD
Enter the name of the site22 that you want use (don't forget to put it in directory pk_run/pk/param) :
Enter the size of the grid will be used for the calculation [default 0.4] :
Enter the residue id of the CYS forming disulfide bonds separated by a comma :
Enter the residue id of the NTER separated with a comma :1
Enter the residue id of the CTER separated with a comma :155
Enter the residue id of the NTNR separated with a comma :
Enter the residue id of the CTNR separated with a comma :
Enter the residue id of the acetylated residu separated with a comma :
Enter the residue id of the CT3 residu separated with a comma :162
Enter the residue id of the CT2 residu separated with a comma :
Enter the residue id of the protonnated asp residu separated with a comma :
Enter the residue id of the protonnated glu residu separated with a comma :
Enter the residue id of the monoanionic phosphoserine separated with a comma :
Enter the residue id of the dianionic phosphoserine separated with a comma :
Enter the nucleic acid id of the 5TER separated with a comma :
Enter the nucleic acid id of the 3TER separated with a comma :
Enter the nucleic acid id of the deoxyribose nucleic acid separated with a comma :
Enter the name of the queue when you want that your UHBD calculation will be submitted :athlons
Enter your e-mail address to know when your UHBD calculation will be finished :cedric.grauffel@gmail.com
Enter the residue id of the NNEU residu separated with a comma :160