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

Fri Mar 18 10:45:20 CET 2016

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 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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