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?
**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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