[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

Fri Mar 18 12:40:54 CET 2016

On 3/18/16 6:31 AM, jkrieger at mrc-lmb.cam.ac.uk wrote:
> Definitely use modeller first. Then go through everything again.
>
> I'm happy you solved the problem with the multiple of 11. Perhaps Justin
> or Mark or someone could comment on why it said that. While it makes sense
> to replace solvent atoms with ions in most cases, I would have thought any
> replacement would work including parts of proteins and ligands.
>

When adding ions, genion assumes the user is replacing a block of uniform 
molecules.  So it checks the first residue in the selected group, and if it 
doesn't match the subsequent residues, it fails.  So if one chooses something 
like the protein or the whole system, the number of atoms in each residue will 
not be the same.  So clearly the user has done something very wrong.

-Justin

> Best wishes
> James
>
>> Thank you for all your suggestion ,ya I did some mistake after adding Na
>> ions   I selected system option (0)
>> As per your suggestion when I selected Sol (13) my problem solved ...Do I
>> need to go for modeller now or should I continue with this ...
>> On 18-Mar-2016 12:41 pm, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>>
>>> I'd suggest creating models with and without residue 508 in the target
>>> sequence. MODELLER should be able to rebuild the loop without residue
>>> 508
>>> and then you won't have long bonds. A hole in a protein is not
>>> physically
>>> or biologically meaningful. Rather a deletion mutation will end up in
>>> the
>>> ribosome inserting the next amino acid and linking it by a normal
>>> peptide
>>> bond.
>>>
>>> You'd then have to set up the system again from the model and I agree
>>> with
>>> Peter that you should check what you're doing against a tutorial to
>>> avoid
>>> the solvent error.
>>>
>>> Best wishes
>>> James
>>>
>>>> My project is on cystic fibrosis 508 del mutation ,what I m trying to
>>> do
>>>> is
>>>> that I have taken nuclear binding domain with 508phenylalanine
>>> (2bbo.pdb)
>>>> and I deleted that 508 phenylalanine to create a similar situation as
>>> what
>>>> occurs in body in case of cystic fibrosis ...after minimization of
>>> this
>>>> protein I ll dock the protein with a corrector ...and will see the
>>> binding
>>>> energy
>>>> On 18-Mar-2016 6:06 am, "Peter Stern" <peter.stern at weizmann.ac.il>
>>> wrote:
>>>>
>>>>> As James said, if you are using Discovery Studio it can model missing
>>>>> atoms and residues.  But why are you deleting a residue?  What do you
>>>>> hope
>>>>> to learn from this?  And don't just ignore missing atoms.
>>>>>
>>>>> I also don't understand the genion error, but I don't think you
>>> reported
>>>>> it exactly.  Didn't genion ask you to choose a solvent group and did
>>> you
>>>>> do
>>>>> that correctly?  I certainly didn't mean that you should choose 1612
>>> sol
>>>>> molecules and 11 Na.  I simply meant that I didn't understand the
>>> error
>>>>> message since 17732 is divisible by 11.  I suspect that you didn't
>>>>> choose
>>>>> the correct group for solvent.
>>>>>
>>>>> Since you are a beginner may I suggest that you use one of the many
>>>>> Gromacs tutorials available choosing one appropriate to what you are
>>>>> trying
>>>>> to do?  I am sure that you can find these easily enough with Google.
>>>>>
>>>>> Best regards?
>>>>> Peter
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>>> On 17 Mar 2016, at 12:27 PM, Pradip Kaur <kaur.pradip253 at gmail.com>
>>>>> wrote:
>>>>>>
>>>>>> actually i m not getting how to proceed futher i m beginner to
>>> GROMACS
>>>>>> ....it would be helpful if you can elaborate the process
>>>>>>
>>>>>>> On 17 March 2016 at 21:54, Pradip Kaur <kaur.pradip253 at gmail.com>
>>>>> wrote:
>>>>>>>
>>>>>>> so should i go for sol molecules :1612
>>>>>>>                          Na :11
>>>>>>>
>>>>>>>> On 17 March 2016 at 21:44, Peter Stern
>>> <peter.stern at weizmann.ac.il>
>>>>> wrote:
>>>>>>>>
>>>>>>>> Missing atoms in GLU 474 is because the coordinates for the GLU
>>> side
>>>>>>>> chain weren't resolved in the crystallographic data and aren't
>>>>> included in
>>>>>>>> the pdb file.  Long bonds are probably because of missing
>>> residues.
>>>>> Check
>>>>>>>> the pdb file for MISSING residues and atoms (listed in the header
>>>>>>>> records).  Also, you can't just delete a residue and let Gromacs
>>>>> think
>>>>> that
>>>>>>>> the preceding and following residues are connected (by an
>>> unphysical
>>>>> "long"
>>>>>>>> bond).  The same goes for missing residues in the pdb file.
>>>>>>>>
>>>>>>>> I hope that the net charge was -5.999 otherwise, why add Na ions.
>>>>> And
>>>>> as
>>>>>>>> far as I know, 11*1612=17732.
>>>>>>>>
>>>>>>>> Peter Stern
>>>>>>>>
>>>>>>>> Sent from my iPad
>>>>>>>>
>>>>>>>> On 17 ×‘×ž×¨×¥ 2016, at 11:08, Pradip Kaur
>>> <kaur.pradip253 at gmail.com
>>>>> <mailto:
>>>>>>>> kaur.pradip253 at gmail.com>> wrote:
>>>>>>>>
>>>>>>>> i am currently working with 2bbo.pdb protein ,i have edited this
>>>>> protein
>>>>>>>> in
>>>>>>>> Discovery studio 4.5 and deleted phenylalanine at 508 position ,
>>> now
>>>>> i
>>>>> m
>>>>>>>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after
>>>>> running
>>>>>>>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it
>>> is
>>>>>>>> showing
>>>>>>>>
>>>>>>>> Warning: Long Bond (161-163 = 1.78456 nm)
>>>>>>>>
>>>>>>>> Warning: Long Bond (840-842 = 0.357037 nm)
>>>>>>>>
>>>>>>>> Warning: Long Bond (2237-2239 = 0.636287 nm)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> WARNING: atom CD is missing in residue GLU 474 in the pdb file
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> WARNING: atom OE1 is missing in residue GLU 474 in the pdb file
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> WARNING: atom OE2 is missing in residue GLU 474 in the pdb file
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -------------------------------------------------------
>>>>>>>>
>>>>>>>> Program pdb2gmx, VERSION 5.0.2
>>>>>>>>
>>>>>>>> Source code file:
>>>>>>>> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
>>>>> line:
>>>>>>>> 1587
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Fatal error:
>>>>>>>>
>>>>>>>> There were 4 missing atoms in molecule Protein_chain_A, if you
>>> want
>>>>> to
>>>>> use
>>>>>>>> this incomplete topology anyhow, use the option -missing
>>>>>>>>
>>>>>>>> For more information and tips for troubleshooting, please check
>>> the
>>>>>>>> GROMACS
>>>>>>>>
>>>>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>>>>>
>>>>>>>>
>>>>>>>> *But  after ignoring missing atoms ,when i am running grompp
>>> command
>>>>> it
>>>>>>>> shows that the system has non zero integral charge of 5.999.*
>>>>>>>>
>>>>>>>> *i have added command genion to neutalise the charge by adding 6
>>> Na
>>>>> ions
>>>>>>>> .After running the command it says that you have generated 17732
>>>>> solvent
>>>>>>>> molecules which are not multiple of 11 .*
>>>>>>>>
>>>>>>>> *can any one help me with this problem*
>>>>>>>> --
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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

==================================================