[gmx-users] grompp command: The solvent group SOL is not continuous

[Justin A. Lemkul]

Halie Shah wrote:
> 
> Hi,
> 
> I am doing an energy minimization of my rsmall protein/ligand complex, 
> following basic drug/enzyme complex EM steps on gromacs 4.0.4. After 
> appending my ligand to my protein (pdb and top file) (also I created the 
> pdb file and itp file for my ligand with dundee prodrg server), and 
> solvating the complex (with commands, "editconf -bt" and "genbox -cp" 
> using spc216.gro water), and running grompp once, I got to the "genion 
> -s" step to neutralize and it gave me the fatal error "The solvent group 
> SOL is not continuous: index[3]=2403, index[4]=2417." Also when I did 
> the earlier grompp command, I got a bunch of warnings saying that my 
> ligand coordinates did not match between my protein topology file and my 
> before ionization protein pdb file...anyway here is the info below...can 
> I be pointed in the right direction?

The error message is pretty explicit.  Your .top and .gro files have to match 
with respect to the order of the atoms (i.e., the .gro has to match [ molecules 
] within the .top).

Check out your .gro; you probably appended the ligand in the wrong spot, had 
crystal waters present, or some other such problem.

-Justin

> 
> **This is the warning I got after running the following command:
> 
> grompp -f em.mdp -c BR6_b4ion.pdb -p BR6.top -o BR6_b4ion.tpr
>     (This was done after solvation of protein+ligand)
> 
> Warning: atom name 2406 in BR6.top and BR6_b4ion.pdb does not match (CAI 
> - N)
> Warning: atom name 2407 in BR6.top and BR6_b4ion.pdb does not match (CAH 
> - HAA)
> Warning: atom name 2408 in BR6.top and BR6_b4ion.pdb does not match (OAK 
> - CA)
> Warning: atom name 2409 in BR6.top and BR6_b4ion.pdb does not match (N - CB)
> Warning: atom name 2410 in BR6.top and BR6_b4ion.pdb does not match (HAA 
> - CAF)
> Warning: atom name 2411 in BR6.top and BR6_b4ion.pdb does not match (CA 
> - OAG)
> Warning: atom name 2412 in BR6.top and BR6_b4ion.pdb does not match (CB - C)
> Warning: atom name 2413 in BR6.top and BR6_b4ion.pdb does not match (CAF 
> - O)
> Warning: atom name 2414 in BR6.top and BR6_b4ion.pdb does not match (OAG 
> - OW)
> Warning: atom name 2415 in BR6.top and BR6_b4ion.pdb does not match (C - 
> HW1)
> Warning: atom name 2416 in BR6.top and BR6_b4ion.pdb does not match (O - 
> HW2)
> 
> WARNING 1 [file BR6.top, line 15394]:
>   16 non-matching atom names
>   atom names from BR6.top will be used
>   atom names from BR6_b4ion.pdb will be ignored
> 
> 
> **This is the warning I got after the genion -s command below:
> 
> genion -s BR6_b4ion.tpr -o BR6_b4em.pdb -nname NA+ -nn 10 -g BR6_ion.log
> 
> Back Off! I just backed up BR6_ion.log to ./#BR6_ion.log.2#
> Reading file BR6_b4ion.tpr, VERSION 4.0.4 (single precision)
> Using a coulomb cut-off of 0.9 nm
> Will try to add 10 Na ions and 0 NA+ ions.
> Select a continuous group of solvent molecules
> Opening library file /opt/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
> Group     0 (      System) has 23473 elements
> Group     1 (     Protein) has  2398 elements
> Group     2 (   Protein-H) has  1914 elements
> Group     3 (     C-alpha) has   240 elements
> Group     4 (    Backbone) has   720 elements
> Group     5 (   MainChain) has   961 elements
> Group     6 (MainChain+Cb) has  1186 elements
> Group     7 ( MainChain+H) has  1187 elements
> Group     8 (   SideChain) has  1211 elements
> Group     9 ( SideChain-H) has   953 elements
> Group    10 ( Prot-Masses) has  2398 elements
> Group    11 ( Non-Protein) has 21075 elements
> Group    12 (        ZN2+) has     2 elements
> Group    13 (         SOL) has 21060 elements
> Group    14 (         DRG) has    13 elements
> Group    15 (       Other) has 21075 elements
> Select a group: 13
> Selected 13: 'SOL'
> 
> -------------------------------------------------------
> Program genion, VERSION 4.0.4
> Source code file: ../../../src/tools/gmx_genion.c, line: 434
> 
> Fatal error:
> The solvent group SOL is not continuous: index[3]=2403, index[4]=2417
> -------------------------------------------------------
> 
> Thanks,
> Halie Shah
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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