majid hasan wrote:
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?
I'm not entirely clear on what you're seeing, but you need to omit step 3 above.
Defining a huge box for a small cube of solvent will lead to incorrect
solvation. genbox will read a solvent configuration and create identical blocks
until the unit cell is full. Defining a larger box in which you place the
solvent prevents this from working.
Positions of molecules inserted with genbox -ci -nmol are random. If you want
to define a specific orientation or position in the box, use editconf
-center/-translate/-rotate as necessary.
-Justin
Thanks,
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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list [email protected]
<mailto:[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]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
