Okay, thanks Justin!. Majid
________________________________ From: Justin A. Lemkul <[email protected]> To: Gromacs Users' List <[email protected]> Sent: Sat, April 16, 2011 6:19:39 PM Subject: Re: [gmx-users] genbox output taking forever to complete Justin A. Lemkul wrote: > > > majid hasan wrote: >> Dear All, >> >> I am trying to add a single strand dna, and single walled carbon nanotube in >> a >>box using the genbox command. After typing following command: >> >> genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o >>cntdna.gro, >> >> I get: Reading solute configuration >> >> Containing 168 atoms in 1 residues >> Initialising van der waals distances... >> >> WARNING: masses and atomic (Van der Waals) radii will be determined >> based on residue and atom names. These numbers can deviate >> from the correct mass and radius of the atom type. >> >> Reading solvent configuration >> "Giving Russians Opium May Alter Current Situation" >> solvent configuration contains 648 atoms in 216 residues >> >> >> and then it takes forever to produce output. >> >> I tried to generate an output with just one molecule in solvent >> (spc216.gro), >>and I ran into same problem. I suspect something is wrong with my solvent >>input >>(file attached). I copied this file from gromacs/tutor/water folder, though >>it >>looks reasonable when I view I view the corresponding .pdb file in rasmol (I >>created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). >> >> Could anyone please guide me about possible issues, and how to resolve them? >> > > You're asking genbox to do far too many things at once. Divide your > procedure >into steps: > > 1. Set a box size using editconf for either the CNT or DNA. I should say "a sensible box size" - a 2x2x2 box barely accommodates the smallest DNA fragment, and then certainly does not leave any room at all to accommodate the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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