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

[jkrieger at mrc-lmb.cam.ac.uk]

You need to use a tool outside GROMACS to model in missing residues.
Discovery studio has capabilities to do this using MODELLER so you could
do that if you're comfortable with that software already (see
http://accelrys.com/services/training/life-science/protein-homology-modeling.html
which I just found through a Google search). I'm not sure what the issue
with the multiple of 11 is though.

Best wishes
James

> 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 במרץ 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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>>
>>
>>
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