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Change.log
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Change.log
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Change in GMXPBSA version 2.1:
January 2017
The compatibility with Gromacs 5 has been adjusted.
March 2016
1) Add the check of the path Gpath Apath Cpath
December 2015
Fixed a bug in the function Average_No_Outliers
June 2015
1) Added the possibility to consider some water molecules as part of the protein, when using "use_topology y".
In input you should indicate the number of water molecules that you are going to consider with the keyword:
water_mol NUM #where NUM is the number of water-molecules.
Note that:
a. In topol.top file these molecules should be listed under "SOL".
b. in the index file these water molecules should be indicated as part of the protein.
i.e.: index relative to
complex -> indicates receptor + water-molecules + ligand
receptor -> indicates receptor + water-molecules
ligand -> indicates only ligand
2) Command "mdrun" has been replaced with "mdrun -ntomp 1 -nt 1" to fix some bugs.
April 2015
1) Added the possibility to perform CAS (on receptor residues) when a custom topology is required for the ligand. A new keyword has been added: "Ltopology_Pff" that must be set to "y". In the INPUT.dat file one must specify the following parameters:
Ltopology_Pff y
use_topology n
itp_ligand name of the itp file for the ligand
ffield (or use_nonstd_ff) indicating the force-field to use for the receptor
If the protonation of the receptor's histidines creates problem (error in the step pdb2gmx/grompp) one should indicate the correct protonation (the one in the xtc file) for each histidine residue of the receptor. In the following example the protonation of the 3 receptor's histidines is indicated (0=HISD; 1=HISE; 2=HISP):
Histidine 0 1 1
This keyword is not mandatory but should be used when errors in pdb2gmx/grompp steps occur.
February 2015
1) in gmxpbsa0.sh replaced lines:
declare -A first
for indexk in $complex $receptor $ligand; do
index_line=`grep -n '^\[ '${indexk}' \]' index.ndx | cut -d: -f1`
index_line=$(($index_line + 1));
first[$indexk]=`head -n ${index_line} index.ndx | tail -n 1 | awk '{print $1}'`
done
if [ ${first[$complex]} -eq ${first[$ligand]} ]; then
......
with the following lines:
complex_line=`grep -n '^\[ '${complex}' \]' index.ndx | cut -d: -f1`
complex_line=$((${complex_line} + 1));
first_c=`head -n ${complex_line} index.ndx | tail -n 1 | awk '{print $1}'`
ligand_line=`grep -n '^\[ '${ligand}' \]' index.ndx | cut -d: -f1`
ligand_line=$((${ligand_line} + 1));
first_l=`head -n ${ligand_line} index.ndx | tail -n 1 | awk '{print $1}'`
if [ ${first_c} -eq ${first_l} ]; then
......
in order to make gmxpbsa0.sh compatible with iOS.
2) Added the option "cutoff-scheme = group" in Mm.mdp in order to make it compatible with gromacs5.x.
Changed lines in print_files.dat from:
function PRINT_MINfile_n {
echo -e "title = Energy in gas \ncpp = /usr/bin/cpp \nconstraints = none \nnsteps = 0 \nnstlist = 0 \nns_type = simple
rlist = 0 \nrcoulomb = 0 \nrvdw = 0 \npbc = no \n;" >> Mm.mdp
}
to:
function PRINT_MINfile_n {
echo -e "title = Energy in gas \ncpp = /usr/bin/cpp \nconstraints = none \nnsteps = 0 \nnstlist = 0 \nns_type = simple
rlist = 0 \nrcoulomb = 0 \nrvdw = 0 \npbc = no \ncutoff-scheme = group \n;" >> Mm.mdp
}
December 2014
1) the option "PBS -l place=free" has been deleted. A new keyword is avaliable called "option_clu2" (optional) to add a new command PBS -l ${option_clu2}
2) backup of gmxpbsa0.sh is added
3) the option "double_p" is deleted. In place of this one there are 2 new options "gmx_prefix" and "gmx_suffix". So, if one has to call the command "mdrun_mpi" instead of "mdrun" should set "gmx_suffix _mpi" in the INPUT.dat file.
September 2014
1) The options "nodes" and "mem" have been eliminated.
A new option is required when using a cluster:
"option_clu", by default it is set to "select=$mnp:ncpus=1:mem=5GB"
when running on a cluster it will be used the command: #PBS -l ${option_clu}
"mnp" is still required, otherwise it will be set to 1 and only 1 APBS job at time will be performed (even if using more processors).
(Example: when using "option_clu = nodes=2:ppn=8" mnp must be set to "mnp=16".)
2) CORRECTIONS TO MAKE GMXPBSA COMPATIBLE TO MAC:
- in gmxpbsa0.sh / function_gmx.dat files, 29 substitutions: &>>STD_ERR0 to >>STD_ERR0 2>&1
- in function_gmx.dat, 2 subs: c=`sed -n '/'$_energy'/{N;p}' to c=`sed -n '/'$_energy'/{N;p;}'
- in function_gmx.dat, 12 subs: sed -i to sed -i -e
- in gmxpbsa0.sh, 8 subs: COMP$counter.log to Pcomp$counter.log
- in gmxpbsa2.sh, 1sub: OUTLIERS=`sort -k 2 -n WARNINGS.dat -u | awk '{if ($1=="FRAME") print $2}'` to OUTLIERS=`sort -k 2 -n WARNINGS.dat -u | awk '{if ($1=="FRAME") printf("%d ",$2);}'`
August 2014
1) Fixed bug related to the use of amino acids with id > 1000.
2) Fixed bug related to the computing of the percentage of failed APBS-jobs.
3) Fixed a bug related to the CAS mutation in the cases in which:
- no chains information are available from xtc/tpr
- the ligand is positioned before the receptor in the pdb
4) Added final message with proper references.
5) Added the possibility to check the GMXPBSA version with the command " sh gmxpbsa[0,1,2].sh -h "
6) Possibility to use "multichain". (Added keyword "multichain", set by default to "n")
Useful if in the pdbs extracted from the trajectory there are more than one chains.
The option "multichain" must be used ONLY if the string TER is not present at the end of each chain in the comp/receptor pdb files.
7) Added the possibility to perform DeltaG CAS calculation on a single protein.
(Added keyword "protein_alone", set by default to "n", and keyword "itp_protein" that must be set only in case of "use_topology=y".)
a) in case of use_topology the following files must be provided:
- topol.top
- file.itp (that must be indicated in the INPUT.dat with the keyword "itp_protein", containing the topology-data relative to the protein that must be investigated).
It could be enough to provide only the topol.top file (no needed itp) at the condition that the topology is related exclusively to the protein that must be analyzed -no solvent-.
b) the line relative to CAS must be: MUTATION RootName ResNumber ResType receptor MutName (receptor can be any thing, but it is important that something is written.)
IMPORTANT: when using the option "protein_alone" in the xtc file provided to GMXPBSA the periodic boundary condition must be treated so to make the broken molecules whole.
(Use: trjconv -pbc whole).
Be careful to use this option! Free energy values are significant only when compared, so provide more files (mutants, folded/unfolded ...)
8) Modified default values for keywords:
keyword old_default new_default
coulomb coul gmx
precF 1 0
linearized n y
9) Many keywords have been added to allow more flexibility with the input files, with the APBS options and to set the option for the cluster. Here there is a list of all the added keywords.
#keyword default meaning
#Input-file related keywoords
name_xtc npt name of the xtc input file
name_tpr npt name of the tpr input file
multichain n see above
protein_alone n see above
itp_protein see above
#APBS-related keywords
extraspace 5 quantity to add (A°) for each side to get fine-grid dimensions
coarsefactor 1.7 factor to get coarse-grid dimensions
grid_spacing 0.5 fine mesh spacing
sdie 80
chgm spl2
srfm smol
srad 1.4
swin 0.3
sdens 10.0
calcforce no
ion_ch_pos 1 positive ion charge in electron units
ion_rad_pos 2.0 positive ion radius
ion_conc_pos 0.15 positive ion concentration
ion_ch_neg -1 negative ion charge in electron units
ion_rad_neg 2.0 negative ion radius
ion_conc_neg 0.15 negative ion concentration
Hsrfm sacc srfm for non-polar calculations
Hpress 0.00 press for non-polar calculations
Hgamma 0.0227 gamma for non-polar calculations
Hdpos 0.20 dpos for non-polar calculations
Hcalcforce total calcforce for non-polar calculations
Hxgrid 0.1 xgrid for non-polar calculations
Hygrid 0.1 ygrid for non-polar calculations
Hzgrid 0.1 zgrid for non-polar calculations
#for the keywords not explained refer to the APBS web site
#CLUSTER-related keywords
nodes 1
mem 5GB
option_clu
option_clu2
#when performing the calculations in a cluster with the PBS queue it use the command:
##PBS -l select=$mnp:ncpus=$nodes:mem=$mem