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

[Peter Stern]

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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