Miguel Quiliano Meza wrote:
*Hi everyone.
I have a problem when I try to run GENION, GROMACS says:
*
WARNING: turning of free energy, will use lambda=0
Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
Using a coulomb cut-off of 0.9 nm
Will try to add 0 Na ions and 15 NA+ ions.
Select a continuous group of solvent molecules
Opening library file /usr/share/gromacs/top/
aminoacids.dat
Group 0 ( System) has 275439 elements
Group 1 ( Protein) has 1722 elements
Group 2 ( Protein-H) has 1371 elements
Group 3 ( C-alpha) has 185 elements
Group 4 ( Backbone) has 555 elements
Group 5 ( MainChain) has 741 elements
Group 6 (MainChain+Cb) has 909 elements
Group 7 ( MainChain+H) has 921 elements
Group 8 ( SideChain) has 801 elements
Group 9 ( SideChain-H) has 630 elements
Group 10 ( Prot-Masses) has 1722 elements
Group 11 ( Non-Protein) has 273717 elements
Group 12 ( ZN) has 1 elements
Group 13 ( SOL) has 273702 elements
Group 14 ( LIG) has 14 elements
Group 15 ( Other) has 273717 elements
Select a group: 13
Selected 13: 'SOL'
-------------------------------------------------------
Program genion, VERSION 3.3.3
Source code file: ../../../../src/tools/gmx_genion.c, line: 429
Fatal error:
The solvent group SOL is not continuous: index[9]=1732, index[10]=1747
-------------------------------------------------------
"Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is."
(Jackie Brown)
*I do not know the reason,the number of residues in top file and pdb
file are the same. The only warning that I saw was when I ran grompp:
*
WARNING 1 [file 1x8a.top, line unknown]:
The largest charge group contains 11 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2 NH, OH, CO2, CO, etc.
*Coincidentally they are some of the atomos of my ligand*
*
I have been reading the web and no-one says nothing about it. I would be
very grateful if someone can help me or give me advices.
Look at your coordinate file. Do you have two separate blocks of solvent, like
crystal waters and then solvent added by genbox (after your zinc and ligand,
perhaps)?
-Justin
Best Regards
MIguel Quiliano*
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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