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

[Peter Stern]

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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