[gmx-users] gromacs file to pqr
aldo jongejan
jongejan at few.vu.nl
Thu Feb 26 18:06:01 CET 2004
Hi Andrea,
I wrote some scripts that convert pdb to MEAD-pqr format.
It is parsing the PARSE charges and radii. However, it might
be critical to PDB atom naming. I just send you the scripts
and PARSE files. Use it at your own risk!
It would be easy to modify (including 'chains' etc) and could be
helpful as a start...
My humble guess is taht there are more sophisticated tools around.
AMBER is able to write pqr files (but you prabaly need .crd and .top
files). Anyway, good luck
aldo
Andrea Carotti wrote:
> Hi gmx-users,
> does anyone know for a program or a script to convert protein structure
> files (pdb, gro...) in pqr format with PARSE charges and radii?
> Thanks for your help
> Andrea
>
> _______________________________________________
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> gmx-users at gromacs.org
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--
###########################################
Aldo Jongejan
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands
e-mail: jongejan at chem.vu.nl
tlf: +31 (0)20 4447612
fax: +31 (0)20 4447610
###########################################
-------------- next part --------------
#! /bin/awk -f
#
# Script to convert a PDB file to a
# pdbq file suitable for MEAD.
# MEAD uses the occupancy column for charges,
# and the original charge column for radii.
# The radii are parsed from the 'parse_radii' file
# found in the MEAD distribution.
# For unidentified atom_names standard vdW radii
# are taken.... (fx in the case of ligands)
#
# AJ - 040501
#
BEGIN \
{ RS = "\n"; j = 0; i = 0; q = 0; r = 0;
if (ARGC < 2)
usage()
file_struct = ARGV[1]
outfile = ARGV[2]
delete ARGV[2]
}
{
RS = "\n";
#####################
# Reading pdb file #
#####################
if (FILENAME == file_struct){
if ($1 == "ATOM" || $1 == "HETATM"){
if (length($3) > 4) {
atom_name[i] = substr($3,1,4)
group[i] = substr($3,5)
residue[i] = $4
X[i] = $5
Y[i] = $6
Z[i] = $7
# charge[i] = $9
}
else {
atom_name[i] = $3
group[i] = $4
residue[i] = $5
X[i] = $6
Y[i] = $7
Z[i] = $8
# charge[i] = $10
}
i++
}
else {
print > outfile
}
}
}
END {
printf "\nAssignment of charges\n******************************\n"
#######################################
# Reading atom radii as used by MEAD #
#######################################
getline < "parse_charges"
getline < "parse_charges"
getline < "parse_charges"
getline < "parse_charges"
getline < "parse_charges"
getline < "parse_charges"
getline < "parse_charges"
while($0 != "" && q <= 622){
parsed_atom[q] = $1
parsed_residue[q] = $2
parsed_charges[q] = $3
q++
getline < "parse_charges"
}
close("parse_charges")
printf " read in charges\n******************************\n"
for (j = 0; j <= i-1; j++){
for (k = 0; k <= q-1; k++){
charge_OK = 0;
if (atom_name[j] == parsed_atom[k] && group[j] == parsed_residue[k]){
charge[j] = parsed_charges[k]
charge_OK = 1; k = q;
}
}
if (charge_OK != 1){
element[j] = substr(atom_name[j],1,1)
if (element[j] == "C"){
charge[j] = 0.555
printf " WARNING - atom name %-4s [%s-%s] default charge assigned\n",\
atom_name[j],group[j],residue[j]
}
if (element[j] == "N"){
charge[j] = -0.400
printf " WARNING - atom name %-4s [%s-%s] default charge assigned\n",\
atom_name[j],group[j],residue[j]
}
if (element[j] == "O"){
charge[j] = -0.500
printf " WARNING - atom name %-4s [%s-%s] default charge assigned\n",\
atom_name[j],group[j],residue[j]
}
if (element[j] == "H"){
charge[j] = 0.200
printf " WARNING - atom name %-4s [%s-%s] default charge assigned\n",\
atom_name[j],group[j],residue[j]
}
}
}
printf "\nAssignment of radii\n******************************\n"
#######################################
# Reading atom radii as used by MEAD #
#######################################
getline < "parse_radii"
getline < "parse_radii"
getline < "parse_radii"
getline < "parse_radii"
getline < "parse_radii"
getline < "parse_radii"
while($0 != ""){
parsed_atom[r] = $1
parsed_residue[r] = $2
parsed_radius[r] = $3
r++
getline < "parse_radii"
}
close("parse_radii")
printf " read in radii\n******************************\n"
for (j = 0; j <= i-1; j++){
for (k = 0; k <= r-1; k++){
radii_OK = 0
if (atom_name[j] == parsed_atom[k] && group[j] == parsed_residue[k]){
radius[j] = parsed_radius[k]
radii_OK = 1; k = r
}
}
if (radii_OK != 1){
element[j] = substr(atom_name[j],1,1)
if (element[j] == "C"){
radius[j] = 2.0
printf " WARNING - atom name %-4s [%s-%s] default radius assigned\n",\
atom_name[j],group[j],residue[j]
}
if (element[j] == "N"){
radius[j] = 1.5
printf " WARNING - atom name %-4s [%s-%s] default radius assigned\n",\
atom_name[j],group[j],residue[j]
}
if (element[j] == "O"){
radius[j] = 1.4
printf " WARNING - atom name %-4s [%s-%s] default radius assigned\n",\
atom_name[j],group[j],residue[j]
}
if (element[j] == "H"){
radius[j] = 0.0
printf " WARNING - atom name %-4s [%s-%s] default radius assigned\n",\
atom_name[j],group[j],residue[j]
}
}
printf "%4s %6s %s%-4s %-4s%5s %2s %8.3f%8.3f%8.3f %6.3f %6.3f\n", \
"ATOM",j+1,"",atom_name[j],group[j],residue[j]," ", \
X[j],Y[j],Z[j],charge[j],radius[j] > outfile
}
printf "TER\nEND\n" > outfile
}
function usage()
{
print "usage: pdb2mead.awk [pdb_file] [outfile]"
exit 1
}
-------------- next part --------------
!crg file created by dfs 2/3/93
!last modification 7/94 to change charged resnames to default
!uses pauling radii with simple charge moments in polar groups
!to match Wolfendon's transfer energies of side chains.
!use with parseres.siz - AJ - added H*3 to comply with other PDB writing programs
atom__resnumbc_charge_
N ALA -0.400
CA ALA -0.000
HN ALA 0.400
HA ALA 0.000
C ALA 0.550
O ALA -0.550
CB ALA 0.000
HB1 ALA 0.000
HB2 ALA 0.000
HB3 ALA 0.000
N ARG -0.400 ! charged arginine
CA ARG -0.000
HN ARG 0.400
HA ARG 0.000
C ARG 0.550
O ARG -0.550
CB ARG 0.000
HB1 ARG 0.000
HB2 ARG 0.000
HB3 ARG 0.000
CG ARG 0.000
HG1 ARG 0.000
HG2 ARG 0.000
HG3 ARG 0.000
CD ARG 0.350
HD1 ARG 0.000
HD2 ARG 0.000
HD3 ARG 0.000
NE ARG -0.350
CZ ARG 0.350
NH1 ARG -0.700
NH2 ARG -0.700
HE ARG 0.450
HH1 ARG 0.400
HH2 ARG 0.400
HH11 ARG 0.400
HH12 ARG 0.400
HH21 ARG 0.400
HH22 ARG 0.400
N AR0 -0.400 !neutral arginine
CA AR0 -0.000
HN AR0 0.400
HA AR0 0.000
C AR0 0.550
O AR0 -0.550
CB AR0 0.000
HB1 AR0 0.000
HB2 AR0 0.000
HB3 AR0 0.000
CG AR0 0.000
HG1 AR0 0.000
HG2 AR0 0.000
HG3 AR0 0.000
CD AR0 0.280
HD1 AR0 0.000
HD2 AR0 0.000
HD3 AR0 0.000
NE AR0 -0.560
HE AR0 0.000
CZ AR0 0.280
NH1 AR0 -0.750
HH1 AR0 0.375
HH2 AR0 0.375
NH2 AR0 -0.750
HH11 AR0 0.375
HH12 AR0 0.375
HH21 AR0 0.375
HH22 AR0 0.375
N ASN -0.400
CA ASN -0.000
HN ASN 0.400
HA ASN 0.000
C ASN 0.550
O ASN -0.550
CB ASN 0.000
HB1 ASN 0.000
HB2 ASN 0.000
HB3 ASN 0.000
CG ASN 0.550
OD1 ASN -0.550
ND2 ASN -0.780
HD1 ASN 0.390
HD2 ASN 0.390
HD21 ASN 0.390
HD22 ASN 0.390
N ASP -0.400 ! charged aspartate
CA ASP -0.000
HN ASP 0.400
HA ASP 0.000
C ASP 0.550
O ASP -0.550
CB ASP 0.000
HB1 ASP 0.000
HB2 ASP 0.000
HB3 ASP 0.000
CG ASP 0.100
OD1 ASP -0.550
OD2 ASP -0.550
N AS0 -0.400 ! neutral aspartate
CA AS0 -0.000
HN AS0 0.400
HA AS0 0.000
C AS0 0.550
O AS0 -0.550
CB AS0 0.000
HB1 AS0 0.000
HB2 AS0 0.000
HB3 AS0 0.000
CG AS0 0.550
OD1 AS0 -0.495
OD2 AS0 -0.490
HD2 AS0 0.435
N CYS -0.400
CA CYS -0.000
HN CYS 0.400
HA CYS 0.000
C CYS 0.550
O CYS -0.550
CB CYS 0.000
HB1 CYS 0.000
HB2 CYS 0.000
HB3 CYS 0.000
SG CYS -0.290
HG CYS 0.290
N CSS -0.400 !cystine in a disulfide bridge
CA CSS -0.000 !no solvation energy to parameterize against
HN CSS 0.400 !using same charge as in methylthiol
HA CSS 0.000 !but on cb and sg
C CSS 0.550
O CSS -0.550
CB CSS 0.290
HB1 CSS 0.000
HB2 CSS 0.000
HB3 CSS 0.000
SG CSS -0.290
N CY- -0.400
CA CY- -0.000
HN CY- 0.400
HA CY- 0.000
C CY- 0.550
O CY- -0.550
CB CY- -0.080
HB1 CY- 0.000
HB2 CY- 0.000
HB3 CY- 0.000
SG CY- -0.920
N GLU -0.400 ! charged glutamic
CA GLU -0.000
HN GLU 0.400
HA GLU 0.000
C GLU 0.550
O GLU -0.550
CB GLU 0.000
HB1 GLU 0.000
HB2 GLU 0.000
HB3 GLU 0.000
CG GLU -0.000
HG1 GLU 0.000
HG2 GLU 0.000
HG3 GLU 0.000
CD GLU 0.100
OE1 GLU -0.550
OE2 GLU -0.550
N GL0 -0.400 ! neutral glutamic
CA GL0 -0.000
HN GL0 0.400
HA GL0 0.000
C GL0 0.550
O GL0 -0.550
CB GL0 0.000
HB1 GL0 0.000
HB2 GL0 0.000
HB3 GL0 0.000
CG GL0 0.000
HG1 GL0 0.000
HG2 GL0 0.000
HG3 GL0 0.000
CD GL0 0.550
OE1 GL0 -0.495
OE2 GL0 -0.490
HE2 GL0 0.435
N GLN -0.400
CA GLN -0.000
HN GLN 0.400
HA GLN 0.000
C GLN 0.550
O GLN -0.550
CB GLN 0.000
HB1 GLN 0.000
HB2 GLN 0.000
HB3 GLN 0.000
CG GLN 0.000
HG1 GLN 0.000
HG2 GLN 0.000
HG3 GLN 0.000
CD GLN 0.550
OE1 GLN -0.550
NE2 GLN -0.780
HE1 GLN 0.390
HE2 GLN 0.390
HE21 GLN 0.390
HE22 GLN 0.390
N GLY -0.400
CA GLY -0.000
HN GLY 0.400
HA1 GLY 0.000
HA2 GLY 0.000
HA3 GLY 0.000
C GLY 0.550
O GLY -0.550
N HIS -0.400
CA HIS -0.000
HN HIS 0.400
HA HIS 0.000
C HIS 0.550
O HIS -0.550
CB HIS 0.125
HB1 HIS 0.000
HB2 HIS 0.000
HB3 HIS 0.000
CG HIS 0.155
ND1 HIS -0.560
CE1 HIS 0.155
NE2 HIS -0.400
CD2 HIS -0.125
HE1 HIS 0.125
HE2 HIS 0.400
HD2 HIS 0.125
N HI+ -0.400
CA HI+ -0.000
HN HI+ 0.400
HA HI+ 0.000
C HI+ 0.550
O HI+ -0.550
CB HI+ 0.125
CG HI+ 0.142
ND1 HI+ -0.350
CE1 HI+ 0.141
NE2 HI+ -0.350
CD2 HI+ 0.142
HB1 HI+ 0.000
HB2 HI+ 0.000
HB3 HI+ 0.000
HD1 HI+ 0.450
HE1 HI+ 0.125
HE2 HI+ 0.450
HD2 HI+ 0.125
N HID -0.400
CA HID -0.000
HN HID 0.400
HA HID 0.000
C HID 0.550
O HID -0.550
CB HID 0.125
HB1 HID 0.000
HB2 HID 0.000
HB3 HID 0.000
CG HID -0.125
ND1 HID -0.400
CE1 HID 0.155
NE2 HID -0.560
CD2 HID 0.155
HD1 HID 0.400
HE1 HID 0.125
HD2 HID 0.125
N ILE -0.400
CA ILE -0.000
HN ILE 0.400
HA ILE 0.000
C ILE 0.550
O ILE -0.550
CB ILE 0.000
HB ILE 0.000
CG2 ILE 0.000
HG1 ILE 0.000
HG2 ILE 0.000
HG3 ILE 0.000
HG21 ILE 0.000
HG22 ILE 0.000
HG23 ILE 0.000
CG1 ILE 0.000
HG11 ILE 0.000
HG12 ILE 0.000
HG13 ILE 0.000
CD1 ILE 0.000
HD1 ILE 0.000
HD2 ILE 0.000
HD3 ILE 0.000
HD11 ILE 0.000
HD12 ILE 0.000
HD13 ILE 0.000
N LEU -0.400
CA LEU -0.000
HN LEU 0.400
HA LEU 0.000
C LEU 0.550
O LEU -0.550
CB LEU 0.000
HB1 LEU 0.000
HB2 LEU 0.000
HB3 LEU 0.000
CG LEU 0.000
HG LEU 0.000
CD1 LEU 0.000
HD1 LEU 0.000
HD2 LEU 0.000
HD3 LEU 0.000
HD11 LEU 0.000
HD12 LEU 0.000
HD13 LEU 0.000
CD2 LEU 0.000
HD21 LEU 0.000
HD22 LEU 0.000
HD23 LEU 0.000
N LYS -0.400 ! charged lysine
CA LYS -0.000
HN LYS 0.400
HA LYS 0.000
C LYS 0.550
O LYS -0.550
CB LYS 0.000
HB1 LYS 0.000
HB2 LYS 0.000
HB3 LYS 0.000
CG LYS 0.000
HG1 LYS 0.000
HG2 LYS 0.000
HG3 LYS 0.000
CD LYS 0.000
HD1 LYS 0.000
HD2 LYS 0.000
HD3 LYS 0.000
CE LYS 0.330
HE1 LYS 0.000
HE2 LYS 0.000
HE3 LYS 0.000
NZ LYS -0.320
HZ1 LYS 0.330
HZ2 LYS 0.330
HZ3 LYS 0.330
N LY0 -0.400 ! neutral lysine
CA LY0 -0.000
HN LY0 0.400
HA LY0 0.000
C LY0 0.550
O LY0 -0.550
CB LY0 0.000
HB1 LY0 0.000
HB2 LY0 0.000
HB3 LY0 0.000
CG LY0 0.000
HG1 LY0 0.000
HG2 LY0 0.000
HG3 LY0 0.000
CD LY0 0.000
HD1 LY0 0.000
HD2 LY0 0.000
HD3 LY0 0.000
CE LY0 0.000
HE1 LY0 0.000
HE2 LY0 0.000
HE3 LY0 0.000
NZ LY0 -0.780
HZ1 LY0 0.390
HZ2 LY0 0.390
N MET -0.400
CA MET -0.000
HN MET 0.400
HA MET 0.000
C MET 0.550
O MET -0.550
CB MET 0.000
HB1 MET 0.000
HB2 MET 0.000
HB3 MET 0.000
CG MET 0.265
HG1 MET 0.000
HG2 MET 0.000
HG3 MET 0.000
SD MET -0.530
CE MET 0.265
HE1 MET 0.000
HE2 MET 0.000
HE3 MET 0.000
N PHE -0.400
CA PHE -0.000
HN PHE 0.400
HA PHE 0.000
C PHE 0.550
O PHE -0.550
CB PHE 0.125
HB1 PHE 0.000
HB2 PHE 0.000
HB3 PHE 0.000
CG PHE -0.125
CD1 PHE -0.125
HD1 PHE 0.125
CE1 PHE -0.125
HE1 PHE 0.125
CZ PHE -0.125
HZ PHE 0.125
CE2 PHE -0.125
HE2 PHE 0.125
CD2 PHE -0.125
HD2 PHE 0.125
N PRO -0.560
CA PRO 0.280
HA PRO 0.000
CD PRO 0.280
HD1 PRO 0.000
HD2 PRO 0.000
HD3 PRO 0.000
C PRO 0.550
O PRO -0.550
CB PRO 0.000
HB1 PRO 0.000
HB2 PRO 0.000
HB3 PRO 0.000
CG PRO 0.000
HG1 PRO 0.000
HG2 PRO 0.000
HG3 PRO 0.000
N SER -0.400
CA SER -0.000
HN SER 0.400
HA SER 0.000
C SER 0.550
O SER -0.550
CB SER 0.000
HB1 SER 0.000
HB2 SER 0.000
HB3 SER 0.000
OG SER -0.490
HG SER 0.490
N THR -0.400
CA THR -0.000
HN THR 0.400
HA THR 0.000
C THR 0.550
O THR -0.550
CB THR 0.000
HB THR 0.000
HB1 THR 0.000
OG1 THR -0.490
HG1 THR 0.490
CG2 THR 0.000
HG2 THR 0.000
HG21 THR 0.000
HG22 THR 0.000
HG23 THR 0.000
N TRP -0.400
CA TRP -0.000
HN TRP 0.400
HA TRP 0.000
C TRP 0.550
O TRP -0.550
CB TRP 0.125
HB1 TRP 0.000
HB2 TRP 0.000
HB3 TRP 0.000
CG TRP -0.125
CD1 TRP -0.125
NE1 TRP -0.400
CE2 TRP 0.000
CD2 TRP -0.000
HD1 TRP 0.125
HE1 TRP 0.400
CE3 TRP -0.125
HE3 TRP 0.125
CZ3 TRP -0.125
HZ3 TRP 0.125
CH2 TRP -0.125
HH2 TRP 0.125
CZ2 TRP -0.125
HZ2 TRP 0.125
N TYR -0.400
CA TYR -0.000
HN TYR 0.400
HA TYR 0.000
C TYR 0.550
O TYR -0.550
CB TYR 0.125
HB1 TYR 0.000
HB2 TYR 0.000
HB3 TYR 0.000
CG TYR -0.125
CD1 TYR -0.125
HD1 TYR 0.125
CE1 TYR -0.125
HE1 TYR 0.125
CZ TYR 0.055
OH TYR -0.490
HH TYR 0.435
CE2 TYR -0.125
HE2 TYR 0.125
CD2 TYR -0.125
HD2 TYR 0.125
N TY- -0.400
CA TY- -0.000
HN TY- 0.400
HA TY- 0.000
C TY- 0.550
O TY- -0.550
CB TY- 0.125
HB1 TY- 0.000
HB2 TY- 0.000
HB3 TY- 0.000
CG TY- -0.195
CD1 TY- -0.195
HD1 TY- 0.125
CE1 TY- -0.195
HE1 TY- 0.125
CZ TY- -0.070
OH TY- -0.580
HH TY- 0.000
CE2 TY- -0.195
HE2 TY- 0.125
CD2 TY- -0.195
HD2 TY- 0.125
N VAL -0.400
CA VAL -0.000
HN VAL 0.400
HA VAL 0.000
C VAL 0.550
O VAL -0.550
CB VAL 0.000
HB VAL 0.000
CG1 VAL 0.000
HG1 VAL 0.000
HG2 VAL 0.000
HG3 VAL 0.000
HG11 VAL 0.000
HG12 VAL 0.000
HG13 VAL 0.000
CG2 VAL 0.000
HG21 VAL 0.000
HG22 VAL 0.000
HG23 VAL 0.000
CA ACE 0.000 !neutral N-cap
HA1 ACE 0.000
HA2 ACE 0.000
HA3 ACE 0.000
C ACE 0.550
O ACE -0.550
N N-M -0.400 !neutral C-cap
CA N-M -0.000
HN1 N-M 0.400
H1 N-M 0.400
HA1 N-M 0.000
HA2 N-M 0.000
HA3 N-M 0.000
N BKN -0.780 !neutral N-terminus
CA BKN -0.000
HN1 BKN 0.390
HN2 BKN 0.390
H1 BKN 0.390
H2 BKN 0.390
HA BKN 0.000
C BKN 0.550
O BKN -0.550
N BK+ -0.320 !charged N-terminus
CA BK+ 0.330 !this is from LYS; alternative: model on ARG)
HN1 BK+ 0.330
HN2 BK+ 0.330
HN3 BK+ 0.330
H1 BK+ 0.330
H2 BK+ 0.330
H3 BK+ 0.330
HA BK+ 0.000
HA BK+ 0.000
C BK+ 0.550
O BK+ -0.550
N BKC -0.400 !neutral C-terminus
HN BKC 0.400
CA BKC -0.000
HA BKC 0.000
C BKC 0.550
O1 BKC -0.495
O2 BKC -0.490
H2 BKC 0.435
N BK- -0.400 !charged C-teminus
HN BK- 0.400
CA BK- -0.000
HA BK- 0.000
C BK- 0.100
O1 BK- -0.550
O2 BK- -0.550
N PRN -0.500 !N-terminal proline, neutral
HN PRN 0.500
CA PRN 0.000
HA PRN 0.000
CD PRN 0.000
HD1 PRN 0.000
HD2 PRN 0.000
C PRN 0.550
O PRN -0.550
CB PRN 0.000
HB1 PRN 0.000
HB2 PRN 0.000
CG PRN 0.000
HG1 PRN 0.000
HG2 PRN 0.000
N PR+ -0.320 !N-terminal proline, charged
HN1 PR+ 0.330
HN2 PR+ 0.330
H1 PR+ 0.330
H2 PR+ 0.330
CA PR+ 0.330
HA PR+ 0.000
CD PR+ 0.330
HD1 PR+ 0.000
HD2 PR+ 0.000
C PR+ 0.550
O PR+ -0.550
CB PR+ 0.000
HB1 PR+ 0.000
HB2 PR+ 0.000
CG PR+ 0.000
HG1 PR+ 0.000
HG2 PR+ 0.000
OH H2O -0.72
HH1 H2O 0.36
HH2 H2O 0.36
-------------- next part --------------
!amino acid radius file by dfs 2/3/93
!last modification 7/94 to change charged resnames to default
!pauling radii to match Wolfendon's transfer energies of side chains
!use with parseres.crg - AJ - added H*3 to comply with other PDB writing programs
atom__res_radius_
N ALA 1.5
CA ALA 2.0
HN ALA 1.0
HA ALA 0.0
C ALA 1.7
O ALA 1.4
CB ALA 2.0
HB1 ALA 0.0
HB2 ALA 0.0
HB3 ALA 0.0
N AR0 1.5 ! neutral arginine
CA AR0 2.0
HN AR0 1.0
HA AR0 0.0
C AR0 1.7
O AR0 1.4
CB AR0 2.0
HB1 AR0 0.0
HB2 AR0 0.0
HB3 AR0 0.0
CG AR0 2.0
HG1 AR0 0.0
HG2 AR0 0.0
HG3 AR0 0.0
CD AR0 2.0
HD1 AR0 0.0
HD2 AR0 0.0
HD3 AR0 0.0
NE AR0 1.5
CZ AR0 1.7
HE AR0 0.0
NH1 AR0 1.5
HH1 AR0 1.0
HH2 AR0 1.0
HH11 AR0 1.0
HH12 AR0 1.0
NH2 AR0 1.5
HH21 AR0 1.0
HH22 AR0 1.0
N ARG 1.5 ! charged arginine
CA ARG 2.0
HN ARG 1.0
HA ARG 0.0
C ARG 1.7
O ARG 1.4
CB ARG 2.0
HB1 ARG 0.0
HB2 ARG 0.0
HB3 ARG 0.0
CG ARG 2.0
HG1 ARG 0.0
HG2 ARG 0.0
HG3 ARG 0.0
CD ARG 2.0
HD1 ARG 0.0
HD2 ARG 0.0
HD3 ARG 0.0
NE ARG 1.5
CZ ARG 1.7
NH1 ARG 1.5
NH2 ARG 1.5
HE ARG 1.0
HH1 ARG 1.0
HH2 ARG 1.0
HH11 ARG 1.0
HH12 ARG 1.0
HH21 ARG 1.0
HH22 ARG 1.0
N ASN 1.5
CA ASN 2.0
HN ASN 1.0
HA ASN 0.0
C ASN 1.7
O ASN 1.4
CB ASN 2.0
HB1 ASN 0.0
HB2 ASN 0.0
HB3 ASN 0.0
CG ASN 1.7
OD1 ASN 1.4
ND2 ASN 1.5
HD1 ASN 1.0
HD2 ASN 1.0
HD21 ASN 1.0
HD22 ASN 1.0
N AS0 1.5 ! aspartate neutral
CA AS0 2.0
HN AS0 1.0
HA AS0 0.0
C AS0 1.7
O AS0 1.4
CB AS0 2.0
HB1 AS0 0.0
HB2 AS0 0.0
HB3 AS0 0.0
CG AS0 1.7
OD1 AS0 1.4
OD2 AS0 1.4
HD2 AS0 1.0
N ASP 1.5 ! aspartate charged
CA ASP 2.0
HN ASP 1.0
HA ASP 0.0
C ASP 1.7
O ASP 1.4
CB ASP 2.0
HB1 ASP 0.0
HB2 ASP 0.0
HB3 ASP 0.0
CG ASP 1.7
OD1 ASP 1.4
OD2 ASP 1.4
N CYS 1.5
CA CYS 2.0
HN CYS 1.0
HA CYS 0.0
C CYS 1.7
O CYS 1.4
CB CYS 2.0
HB1 CYS 0.0
HB2 CYS 0.0
HB3 CYS 0.0
SG CYS 1.85
HG CYS 1.0
N CSS 1.5 !cystine in disulfide bridge
CA CSS 2.0
HN CSS 1.0
HA CSS 0.0
C CSS 1.7
O CSS 1.4
CB CSS 2.0
HB1 CSS 0.0
HB2 CSS 0.0
HB3 CSS 0.0
SG CSS 1.85
N CY- 1.5
CA CY- 2.0
HN CY- 1.0
HA CY- 0.0
C CY- 1.7
O CY- 1.4
CB CY- 2.0
HB1 CY- 0.0
HB2 CY- 0.0
HB3 CY- 0.0
SG CY- 1.85
N GL0 1.5 ! neutral glutamic
CA GL0 2.0
HN GL0 1.0
HA GL0 0.0
C GL0 1.7
O GL0 1.4
CB GL0 2.0
HB1 GL0 0.0
HB2 GL0 0.0
HB3 GL0 0.0
CG GL0 2.0
HG1 GL0 0.0
HG2 GL0 0.0
HG3 GL0 0.0
CD GL0 1.7
OE1 GL0 1.4
OE2 GL0 1.4
HE2 GL0 1.0
N GLU 1.5 ! charged glutamic
CA GLU 2.0
HN GLU 1.0
HA GLU 0.0
C GLU 1.7
O GLU 1.4
CB GLU 2.0
HB1 GLU 0.0
HB2 GLU 0.0
HB3 GLU 0.0
CG GLU 2.0
HG1 GLU 0.0
HG2 GLU 0.0
HG3 GLU 0.0
CD GLU 1.7
OE1 GLU 1.4
OE2 GLU 1.4
N GLN 1.5
CA GLN 2.0
HN GLN 1.0
HA GLN 0.0
C GLN 1.7
O GLN 1.4
CB GLN 2.0
HB1 GLN 0.0
HB2 GLN 0.0
HB3 GLN 0.0
CG GLN 2.0
HG1 GLN 0.0
HG2 GLN 0.0
HG3 GLN 0.0
CD GLN 1.7
OE1 GLN 1.4
NE2 GLN 1.5
HE1 GLN 1.0
HE2 GLN 1.0
HE21 GLN 1.0
HE22 GLN 1.0
N GLY 1.5
CA GLY 2.0
HN GLY 1.0
HA1 GLY 0.0
HA2 GLY 0.0
HA3 GLY 0.0
C GLY 1.7
O GLY 1.4
N HIS 1.5
CA HIS 2.0
HN HIS 1.0
HA HIS 0.0
C HIS 1.7
O HIS 1.4
CB HIS 2.0
HB1 HIS 0.0
HB2 HIS 0.0
HB3 HIS 0.0
CG HIS 1.7
ND1 HIS 1.5
CE1 HIS 1.7
NE2 HIS 1.5
CD2 HIS 1.7
HE1 HIS 1.0
HE2 HIS 1.0
HD2 HIS 1.0
N HI+ 1.5
CA HI+ 2.0
HN HI+ 1.0
HA HI+ 0.0
C HI+ 1.7
O HI+ 1.4
CB HI+ 2.0
CG HI+ 1.7
ND1 HI+ 1.5
CE1 HI+ 1.7
NE2 HI+ 1.5
CD2 HI+ 1.7
HB1 HI+ 0.0
HB2 HI+ 0.0
HB3 HI+ 0.0
HD1 HI+ 1.0
HE1 HI+ 1.0
HE2 HI+ 1.0
HD2 HI+ 1.0
N HID 1.5
CA HID 2.0
HN HID 1.0
HA HID 0.0
C HID 1.7
O HID 1.4
CB HID 2.0
HB1 HID 0.0
HB2 HID 0.0
HB3 HID 0.0
CG HID 1.7
ND1 HID 1.5
CE1 HID 1.7
NE2 HID 1.5
CD2 HID 1.7
HD1 HID 1.0
HE1 HID 1.0
HD2 HID 1.0
N ILE 1.5
CA ILE 2.0
HN ILE 1.0
HA ILE 0.0
C ILE 1.7
O ILE 1.4
CB ILE 2.0
HB ILE 0.0
CG2 ILE 2.0
HG1 ILE 0.0
HG2 ILE 0.0
HG3 ILE 0.0
HG21 ILE 0.0
HG22 ILE 0.0
HG23 ILE 0.0
CG1 ILE 2.0
HG11 ILE 0.0
HG12 ILE 0.0
HG13 ILE 0.0
CD1 ILE 2.0
HD1 ILE 0.0
HD2 ILE 0.0
HD3 ILE 0.0
HD11 ILE 0.0
HD12 ILE 0.0
HD13 ILE 0.0
N LEU 1.5
CA LEU 2.0
HN LEU 1.0
HA LEU 0.0
C LEU 1.7
O LEU 1.4
CB LEU 2.0
HB1 LEU 0.0
HB2 LEU 0.0
HB3 LEU 0.0
CG LEU 2.0
HG LEU 0.0
CD1 LEU 2.0
HD1 LEU 0.0
HD2 LEU 0.0
HD3 LEU 0.0
HD11 LEU 0.0
HD12 LEU 0.0
HD13 LEU 0.0
CD2 LEU 2.0
HD21 LEU 0.0
HD22 LEU 0.0
HD23 LEU 0.0
N LY0 1.5 ! lysine neutral
CA LY0 2.0
HN LY0 1.0
HA LY0 0.0
C LY0 1.7
O LY0 1.4
CB LY0 2.0
HB1 LY0 0.0
HB2 LY0 0.0
HB3 LY0 0.0
CG LY0 2.0
HG1 LY0 0.0
HG2 LY0 0.0
HG3 LY0 0.0
CD LY0 2.0
HD1 LY0 0.0
HD2 LY0 0.0
HD3 LY0 0.0
CE LY0 2.0
HE1 LY0 0.0
HE2 LY0 0.0
HE3 LY0 0.0
NZ LY0 1.5
HZ1 LY0 1.0
HZ2 LY0 1.0
N LYS 1.5 ! lysine charged
CA LYS 2.0
HN LYS 1.0
HA LYS 0.0
C LYS 1.7
O LYS 1.4
CB LYS 2.0
HB1 LYS 0.0
HB2 LYS 0.0
HB3 LYS 0.0
CG LYS 2.0
HG1 LYS 0.0
HG2 LYS 0.0
HG3 LYS 0.0
CD LYS 2.0
HD1 LYS 0.0
HD2 LYS 0.0
HD3 LYS 0.0
CE LYS 2.0
HE1 LYS 0.0
HE2 LYS 0.0
HE3 LYS 0.0
NZ LYS 2.0
HZ1 LYS 0.0
HZ2 LYS 0.0
HZ3 LYS 0.0
N MET 1.5
CA MET 2.0
HN MET 1.0
HA MET 0.0
C MET 1.7
O MET 1.4
CB MET 2.0
HB1 MET 0.0
HB2 MET 0.0
HB3 MET 0.0
CG MET 2.0
HG1 MET 0.0
HG2 MET 0.0
HG3 MET 0.0
SD MET 1.85
CE MET 2.0
HE1 MET 0.0
HE2 MET 0.0
HE3 MET 0.0
N PHE 1.5
CA PHE 2.0
HN PHE 1.0
HA PHE 0.0
C PHE 1.7
O PHE 1.4
CB PHE 2.0
HB1 PHE 0.0
HB2 PHE 0.0
HB3 PHE 0.0
CG PHE 1.7
CD1 PHE 1.7
HD1 PHE 1.0
CE1 PHE 1.7
HE1 PHE 1.0
CZ PHE 1.7
HZ PHE 1.0
CE2 PHE 1.7
HE2 PHE 1.0
CD2 PHE 1.7
HD2 PHE 1.0
N PRO 1.5
CA PRO 2.0
HA PRO 0.0
CD PRO 2.0
HD1 PRO 0.0
HD2 PRO 0.0
HD3 PRO 0.0
C PRO 1.7
O PRO 1.4
CB PRO 2.0
HB1 PRO 0.0
HB2 PRO 0.0
HB3 PRO 0.0
CG PRO 2.0
HG1 PRO 0.0
HG2 PRO 0.0
HG3 PRO 0.0
N SER 1.5
CA SER 2.0
HN SER 1.0
HA SER 0.0
C SER 1.7
O SER 1.4
CB SER 2.0
HB1 SER 0.0
HB2 SER 0.0
HB3 SER 0.0
OG SER 1.4
HG SER 1.0
N THR 1.5
CA THR 2.0
HN THR 1.0
HA THR 0.0
C THR 1.7
O THR 1.4
CB THR 2.0
HB THR 0.0
OG1 THR 1.4
HG1 THR 1.0
CG2 THR 2.0
HG2 THR 0.0
HG21 THR 0.0
HG22 THR 0.0
HG23 THR 0.0
N TRP 1.5
CA TRP 2.0
HN TRP 1.0
HA TRP 0.0
C TRP 1.7
O TRP 1.4
CB TRP 2.0
HB1 TRP 0.0
HB2 TRP 0.0
HB3 TRP 0.0
CG TRP 1.7
CD1 TRP 1.7
NE1 TRP 1.5
CE2 TRP 1.7
CD2 TRP 1.7
HD1 TRP 1.0
HE1 TRP 1.0
CE3 TRP 1.7
HE3 TRP 1.0
CZ3 TRP 1.7
HZ3 TRP 1.0
CH2 TRP 1.7
HH2 TRP 1.0
CZ2 TRP 1.7
HZ2 TRP 1.0
N TYR 1.5
CA TYR 2.0
HN TYR 1.0
HA TYR 0.0
C TYR 1.7
O TYR 1.4
CB TYR 2.0
HB1 TYR 0.0
HB2 TYR 0.0
HB3 TYR 0.0
CG TYR 1.7
CD1 TYR 1.7
HD1 TYR 1.0
CE1 TYR 1.7
HE1 TYR 1.0
CZ TYR 1.7
OH TYR 1.4
HH TYR 1.0
CE2 TYR 1.7
HE2 TYR 1.0
CD2 TYR 1.7
HD2 TYR 1.0
N TY- 1.5
CA TY- 2.0
HN TY- 1.0
HA TY- 0.0
C TY- 1.7
O TY- 1.4
CB TY- 2.0
HB1 TY- 0.0
HB2 TY- 0.0
HB3 TY- 0.0
CG TY- 1.7
CD1 TY- 1.7
HD1 TY- 1.0
CE1 TY- 1.7
HE1 TY- 1.0
CZ TY- 1.7
OH TY- 1.4
CE2 TY- 1.7
HE2 TY- 1.0
CD2 TY- 1.7
HD2 TY- 1.0
N VAL 1.5
CA VAL 2.0
HN VAL 1.0
HA VAL 0.0
C VAL 1.7
O VAL 1.4
CB VAL 2.0
HB VAL 0.0
CG1 VAL 2.0
HG1 VAL 0.0
HG2 VAL 0.0
HG3 VAL 0.0
HG11 VAL 0.0
HG12 VAL 0.0
HG13 VAL 0.0
CG2 VAL 2.0
HG21 VAL 0.0
HG22 VAL 0.0
HG23 VAL 0.0
CA ACE 2.0 !neutral N-cap
HA1 ACE 0.0
HA2 ACE 0.0
HA3 ACE 0.0
C ACE 1.7
O ACE 1.4
N N-M 1.5 !neutral C-cap
CA N-M 2.0
HN1 N-M 1.0
H1 N-M 1.0
HA1 N-M 0.0
HA2 N-M 0.0
HA3 N-M 0.0
N BKN 1.5 !neutral N-terminus
CA BKN 2.0
HN1 BKN 1.0
HN2 BKN 1.0
H1 BKN 1.0
H2 BKN 1.0
HA BKN 0.0
C BKN 1.7
O BKN 1.4
N BK+ 2.0 !charged N-terminus
CA BK+ 2.0
HN1 BK+ 0.0
HN2 BK+ 0.0
HN3 BK+ 0.0
H1 BK+ 0.0
H2 BK+ 0.0
H3 BK+ 0.0
HA BK+ 0.0
C BK+ 1.7
O BK+ 1.4
N BKC 1.5 !neutral C-terminus
HN BKC 1.0
CA BKC 2.0
HA BKC 0.0
C BKC 1.7
O1 BKC 1.4
O2 BKC 1.4
H2 BKC 1.0
N BK- 1.5 !charged C-terminus
HN BK- 1.0
CA BK- 2.0
HA BK- 0.0
C BK- 1.7
O1 BK- 1.4
O2 BK- 1.4
N PRN 1.5 !N-terminal proline, neutral
HN PRN 1.0
CA PRN 2.0
HA PRN 0.0
CD PRN 2.0
HD1 PRN 0.0
HD2 PRN 0.0
C PRN 1.7
O PRN 1.4
CB PRN 2.0
HB1 PRN 0.0
HB2 PRN 0.0
CG PRN 2.0
HG1 PRN 0.0
HG2 PRN 0.0
N PR+ 2.0 !N-terminal proline, charged
HN1 PR+ 0.0
HN2 PR+ 0.0
H1 PR+ 0.0
H2 PR+ 0.0
CA PR+ 2.0
HA PR+ 0.0
CD PR+ 2.0
HD1 PR+ 0.0
HD2 PR+ 0.0
C PR+ 1.7
O PR+ 1.4
CB PR+ 2.0
HB1 PR+ 0.0
HB2 PR+ 0.0
CG PR+ 2.0
HG1 PR+ 0.0
HG2 PR+ 0.0
OH H2O 1.4
HH1 H2O 1.0
HH2 H2O 1.0
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