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

[Pradip Kaur]

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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