diff options
| author | Drobot Viktor | 2019-04-09 17:44:15 +0300 |
|---|---|---|
| committer | Drobot Viktor | 2019-04-09 17:44:15 +0300 |
| commit | d642ad57d9c7af2166badd3d7ddbf79bca6f9950 (patch) | |
| tree | 84218d4a91da887a6c97e8fd514d739ca811e728 | |
| parent | 73049794b22916b8e95fe679dd8e4803d24a5c4f (diff) | |
| download | aur-d642ad57d9c7af2166badd3d7ddbf79bca6f9950.tar.gz | |
Extended AMBER forcefield. Added profile script
| -rw-r--r-- | PKGBUILD | 21 | ||||
| -rw-r--r-- | amber_dat.patch | 36 | ||||
| -rw-r--r-- | pdb2pqr.sh | 2 |
3 files changed, 55 insertions, 4 deletions
@@ -1,17 +1,23 @@ # Maintainer: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com pkgname=pdb2pqr pkgver=2.1.1 -pkgrel=3 +pkgrel=4 pkgdesc="Electrostatic and solvation properties for complex molecules" arch=(x86_64 i686) url="http://www.poissonboltzmann.org/" license=('MIT') depends=('swig' 'python2' 'python2-networkx' 'python2-numpy' 'apbs') -makedepends=('git' 'gcc') +makedepends=('git' 'gcc' 'patch') +optdepends=("pymol-python2: APBSTools plugin support" + "python2-pmw: APBSTools plugin support") source=("git+https://github.com/Electrostatics/apbs-pdb2pqr.git#commit=433a1984a632b396bda11416b757d00e4ef5189e" - "pdb2pqr.patch") + "pdb2pqr.patch" + "amber_dat.patch" + "pdb2pqr.sh") md5sums=('SKIP' - '19cb8e794d49e4d2bc04df54a895f3ad') + '19cb8e794d49e4d2bc04df54a895f3ad' + '2f2e838377ee176a22f9c4ac313714f5' + '4533f9bb6ce2d94ed2d97c0a05e6b071') prepare() { cd ${srcdir}/apbs-pdb2pqr/pdb2pqr @@ -32,4 +38,11 @@ package() { python2 scons/scons.py PREFIX=${pkgdir}/opt/pdb2pqr install touch ${pkgdir}/opt/pdb2pqr/__init__.py + + # add non-standard residues to AMBER forcefield (N-terminal serine, bromoacetylserine, calcium) + cd ${pkgdir}/opt/pdb2pqr/dat + patch -Np0 -i ${srcdir}/amber_dat.patch + + # install profile script for proper APBSTools plugins usage + install -Dm644 ${srcdir}/pdb2pqr.sh ${pkgdir}/etc/profile.d/pdb2pqr.sh } diff --git a/amber_dat.patch b/amber_dat.patch new file mode 100644 index 000000000000..e4ef9aec4609 --- /dev/null +++ b/amber_dat.patch @@ -0,0 +1,36 @@ +--- AMBER.DAT 2019-04-05 21:38:47.000000000 +0300 ++++ AMBER.DAT 2019-04-09 14:03:29.712379551 +0300 +@@ -2257,3 +2257,33 @@ + RUN H3T 0.437600 0.0000 HO + WAT HW 0.417000 0.0000 HW + WAT OW -0.834000 1.6612 OW ++NTS N -0.920500 1.8240 N3 ++NTS H1 0.362800 0.6000 H ++NTS H2 0.362800 0.6000 H ++NTS CA 0.029300 1.9080 CT ++NTS HA 0.104200 1.3870 H1 ++NTS CB 0.075000 1.9080 CT ++NTS HB2 0.073700 1.3870 H1 ++NTS HB3 0.073700 1.3870 H1 ++NTS OG -0.619500 1.7210 OH ++NTS HG 0.414400 0.0000 HO ++NTS C 0.616300 1.9080 C ++NTS O -0.572200 1.6612 O ++BAS N -0.937900 1.8240 NT ++BAS H1 0.379400 0.6000 H ++BAS H2 0.379400 0.6000 H ++BAS CA 0.071300 1.9080 CX ++BAS HA 0.137400 1.3870 H1 ++BAS CB 0.091800 1.9080 CT ++BAS HB2 0.041800 1.3870 H1 ++BAS HB3 0.041800 1.3870 H1 ++BAS OG -0.367800 1.6837 OS ++BAS CD 0.779500 1.9080 C ++BAS CE2 -0.534700 1.9080 CT ++BAS HE2 0.261100 1.3870 H1 ++BAS HE3 0.261100 1.3870 H1 ++BAS BR -0.059200 2.22 Br ++BAS OE1 -0.535000 1.6612 O ++BAS C 0.527200 1.9080 C ++BAS O -0.537200 1.6612 O ++CA CA 2.0 1.649 Ca2+ diff --git a/pdb2pqr.sh b/pdb2pqr.sh new file mode 100644 index 000000000000..c68c419e14b8 --- /dev/null +++ b/pdb2pqr.sh @@ -0,0 +1,2 @@ +export APBS_PSIZE_DIR=/usr/share/apbs/tools/manip +export APBS_PDB2PQR_DIR=/opt/pdb2pqr |