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

[Pradip Kaur]

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*