Okay, so I divided the procedure in three steps, and this does produce output immediately. But it seems that it doesn't put second molecule inside the box. Here is the what I am doing:
1. editconf -f ssgcg.pdb -o ssgcg.gro -box 20 20 20 2. genbox -cp ssgcg.gro -ci cntcapped.pdb -nmol 1 -o cntdna.gro 3. editconf -f spc216.pdb -o spc216.gro -box 20 20 20 4. genbox -cp cntdna.gro -cs spc216.gro -o solvated.gro 5. editconf -f solvated.gro -o solvated.pdb I tried cubic boxes of different lenghts (10, 20, 100), but when I see the final file in solvated.pdb in rasmol, it seems that it puts dna, and cnt at a distance equal to the specified length of the box, and the water molecules are all clustered around dna only. I also tried to create a box of lenght 100 20 20 and align dna along 1 0 0, but I still got the similar final output. My question is, what determines the distance between molecules inside the box, and how can I make sure that they are placed at a reasonable distance inside the solvent? Thanks, Majid ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Gromacs Users' List <gmx-users@gromacs.org> 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists