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

[Pradip Kaur]

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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>