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

Fri Mar 18 04:50:54 CET 2016

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 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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