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

Fri Mar 18 08:11:33 CET 2016

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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