<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt">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.<br>Here is the what I am doing:<br><br>1. editconf -f ssgcg.pdb -o ssgcg.gro -box 20 20 20 <br>2. genbox -cp ssgcg.gro -ci cntcapped.pdb -nmol 1 -o cntdna.gro<br>3. editconf -f spc216.pdb -o spc216.gro -box 20 20 20<br>4. genbox -cp cntdna.gro -cs spc216.gro -o solvated.gro<br>5. editconf -f solvated.gro -o solvated.pdb<br><br>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.<br><br>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. <br><br>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?<br><br>Thanks,<br>Majid<br><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Gromacs Users' List <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sat, April 16, 2011 6:19:39 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] genbox output taking forever to complete<br></font><br>
<br><br>Justin A. Lemkul wrote:<br>> <br>> <br>> majid hasan wrote:<br>>> Dear All,<br>>> <br>>> 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:<br>>> <br>>> genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro,<br>>> <br>>> I get: Reading solute configuration<br>>> <br>>> Containing 168 atoms in 1 residues<br>>> Initialising van der waals distances...<br>>> <br>>> WARNING: masses and atomic (Van der Waals) radii will be determined<br>>> based on residue and atom names. These numbers can deviate<br>>> from the correct mass and radius of the atom type.<br>>> <br>>> Reading solvent configuration<br>>> "Giving Russians Opium May Alter Current
Situation"<br>>> solvent configuration contains 648 atoms in 216 residues<br>>> <br>>> <br>>> and then it takes forever to produce output.<br>>> <br>>> 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).<br>>> <br>>> Could anyone please guide me about possible issues, and how to resolve them?<br>>> <br>> <br>> You're asking genbox to do far too many things at once. Divide your procedure into steps:<br>> <br>> 1. Set a box size using editconf for either the CNT or DNA.<br><br>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.<br><br><span><a target="_blank" href="http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention">http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention</a></span><br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org"
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