[gmx-users] Fwd: Questions for the forum

Thu Oct 13 16:39:14 CEST 2016

I started with a pdb file of the protein, 5000 residues, no solvent,
crystallographic structure.

Generated the .gro file, opting for the AMBER99SB force field (option 5):

gmx pdb2gmx -f YYY.pdb -o YYY_GROMACS.gro -water tip3p -ignh (opted
for ignh as I was having trouble with differences in nomemclature)

defined box:

gmx editconf -f YYY_GROMACS.gro -o YYY_newbox.gro -c -d 1.2 -bt dodechaedron

solvation:

gmx solvate -cp YYY_GROMACS_newbox.gro -cs spc216.gro -o
YYY_GROMACS_newboxsolv.gro -p topol.top

add ions:

gmx grompp -f ions.mdp -c YYY_newboxsolv.gro -p topol.top -o ions.tpr

gmx genion -s ions.tpr -o YYY_newboxsolv_ions.gro -p topol.top -pname
NA -np 76 (the charge was -76)  (chose group 13 like the tutorial,
SOL)

at this point, my topol is:
[ molecules ]
; Compound        #mols
Protein_chain_X     1
SOL         766582
NA               76

and from this point i went on with minimization and so on.

2016-10-13 14:49 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 10/13/16 9:45 AM, Matilde Viegas wrote:
>
>> Of course, sorry!
>> I followed your lyzosyme tutorial, the exact same commands, only addapting
>> it to my system (force field, tip3p water, just like I did on AMBER), box
>> was dodechaedron, 1.2nm. I didn't alter anything beside that... My enzyme
>> is around 72 thousand atoms, after adding the solvation box, it goes up to
>> 2.5 million atoms.
>>
>>
> You need to provide your exact commands, copied and pasted from the
> terminal. You can't just say you did my tutorial, because there's a lot of
> differences in what you actually did and what's in that example.
>
> One thing that is unclear is if you're trying to import an
> already-solvated system from AMBER into GROMACS.  If you are, then you
> shouldn't be re-sizing the box or adding any more water.  But again, only
> your exact commands and descriptions of file contents will tell us anything
> productive.
>
> -Justin
>
>
> 2016-10-13 14:40 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>>
>>> On 10/13/16 9:38 AM, Matilde Viegas wrote:
>>>
>>> Yes, I noticed that! I said 10, referring to angstrom, in the input I had
>>>> 1.0nm.
>>>>
>>>> So you probably think it is only some error in the input, not really
>>>> something I can tackle, right? I really can't figure it out...
>>>>
>>>>
>>>> Without seeing your exact sequence of commands, there's nothing we can
>>> do
>>> to help.  The only thing consistent with having an unexpected
>>> million-atom
>>> system is that you set up the box incorrectly with editconf.  But you
>>> haven't told us exactly what you've done...
>>>
>>> -Justin
>>>
>>>
>>> Thank you for your time, Justin
>>>
>>>>
>>>> 2016-10-13 13:04 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>>>
>>>>
>>>>
>>>>> On 10/13/16 7:34 AM, Matilde Viegas wrote:
>>>>>
>>>>> I tried to downzise to 10 and yet the reduction was very little. I was
>>>>>
>>>>>> just
>>>>>> trying t understand how can the difference between the same systems,
>>>>>> using
>>>>>> either AMBER or GROMACS, can be of 1 million atoms...
>>>>>>
>>>>>>
>>>>>> GROMACS uses SI units, so distances/box vectors are specified in nm,
>>>>>> not
>>>>>>
>>>>> Angstrom.  See Chapter 2 of the manual for unit conventions.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>> 2016-10-13 12:27 GMT+01:00 Dd H <ddhecnu at gmail.com>:
>>>>>
>>>>>
>>>>>> You can reduce your box size to get a smaller system.
>>>>>>
>>>>>>
>>>>>>> On 13 October 2016 at 17:41, Matilde Viegas <
>>>>>>> matildefrviegas at gmail.com
>>>>>>>
>>>>>>>>
>>>>>>>> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>>
>>>>>>>> my name is Matilde. This is my first time using GROMACS. I'm
>>>>>>>> switching
>>>>>>>>
>>>>>>>> from
>>>>>>>>
>>>>>>>
>>>>>>> AMBER to GROMACS however I'm having some trouble reproducing my
>>>>>>> system:
>>>>>>>
>>>>>>>>
>>>>>>>> In AMBER, I'm working with a 5000 residues protein, a water box
>>>>>>>> (TIP3)
>>>>>>>> of
>>>>>>>> 12A, roughly 1.5 million atoms total. I tried building the same
>>>>>>>> system
>>>>>>>> in
>>>>>>>> GROMACS, cubic box, 12A, same protein, however I obtain a 2.5
>>>>>>>> million
>>>>>>>>
>>>>>>>> atoms
>>>>>>>>
>>>>>>>
>>>>>>> system. Is there a way I can reduce the number of atoms?
>>>>>>>
>>>>>>>>
>>>>>>>> Thank you in advance,
>>>>>>>> Matilde
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
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>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>> Gromacs Users mailing list
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>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>
>>>>>
>>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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>