From b9761296c3e966bde033bf19ced7ef7f8132e426 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 6 Feb 2026 10:04:10 -0500 Subject: [PATCH 1/3] Need to separate ranges with '|' (or) instead of comma --- AmberMdPrep.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/AmberMdPrep.sh b/AmberMdPrep.sh index d1d8c19..db05696 100755 --- a/AmberMdPrep.sh +++ b/AmberMdPrep.sh @@ -595,12 +595,12 @@ while read MLINE ; do if [ -z "$HEAVYMASK" ] ; then HEAVYMASK=":$resrange&!@H=" else - HEAVYMASK="$HEAVYMASK,:$resrange&!@H=" + HEAVYMASK="$HEAVYMASK|:$resrange&!@H=" fi if [ -z "$BACKBONEMASK" ] ; then BACKBONEMASK=":$resrange$bbatoms" else - BACKBONEMASK="$BACKBONEMASK,:$resrange$bbatoms" + BACKBONEMASK="$BACKBONEMASK|:$resrange$bbatoms" fi fi done < $TMPMASK From 69b2d32e3d1e0d4bcca0dbee985c48e412a47f1e Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 6 Feb 2026 10:05:07 -0500 Subject: [PATCH 2/3] Update with fixed masks --- test/modified.residues/Save/step1.in | 2 +- test/modified.residues/Save/step2.in | 2 +- test/modified.residues/Save/step3.in | 2 +- test/modified.residues/Save/step4.in | 2 +- test/modified.residues/Save/step6.in | 2 +- test/modified.residues/Save/step7.in | 2 +- test/modified.residues/Save/step8.in | 2 +- test/modified.residues/test.out.save | 4 ++-- 8 files changed, 9 insertions(+), 9 deletions(-) diff --git a/test/modified.residues/Save/step1.in b/test/modified.residues/Save/step1.in index 2a2132e..9a4d984 100644 --- a/test/modified.residues/Save/step1.in +++ b/test/modified.residues/Save/step1.in @@ -3,5 +3,5 @@ Minimization: step1.in imin = 1, ntmin = 2, maxcyc = 1000, ncyc = 10, ntwx = 500, ioutfm = 1, ntxo = 2, ntpr = 50, ntwr = 500, ntc = 1, ntf = 1, ntb = 1, cut = 8.0, - ntr = 1, restraintmask = ":1-5&!@H=,:8-13&!@H=", restraint_wt = 5.0, + ntr = 1, restraintmask = ":1-5&!@H=|:8-13&!@H=", restraint_wt = 5.0, &end diff --git a/test/modified.residues/Save/step2.in b/test/modified.residues/Save/step2.in index b5a1082..7277906 100644 --- a/test/modified.residues/Save/step2.in +++ b/test/modified.residues/Save/step2.in @@ -6,5 +6,5 @@ MD: step2.in iwrap = 0, nscm = 0, ntc = 2, ntf = 2, ntb = 1, cut = 8.0, ntt = 3, gamma_ln = 5, temp0 = 300, tempi = 300, - ntr = 1, restraintmask = ":1-5&!@H=,:8-13&!@H=", restraint_wt = 5.0, + ntr = 1, restraintmask = ":1-5&!@H=|:8-13&!@H=", restraint_wt = 5.0, &end diff --git a/test/modified.residues/Save/step3.in b/test/modified.residues/Save/step3.in index cf1c618..9ae596b 100644 --- a/test/modified.residues/Save/step3.in +++ b/test/modified.residues/Save/step3.in @@ -3,5 +3,5 @@ Minimization: step3.in imin = 1, ntmin = 2, maxcyc = 1000, ncyc = 10, ntwx = 500, ioutfm = 1, ntxo = 2, ntpr = 50, ntwr = 500, ntc = 1, ntf = 1, ntb = 1, cut = 8.0, - ntr = 1, restraintmask = ":1-5&!@H=,:8-13&!@H=", restraint_wt = 2.0, + ntr = 1, restraintmask = ":1-5&!@H=|:8-13&!@H=", restraint_wt = 2.0, &end diff --git a/test/modified.residues/Save/step4.in b/test/modified.residues/Save/step4.in index 74a46f2..2f55376 100644 --- a/test/modified.residues/Save/step4.in +++ b/test/modified.residues/Save/step4.in @@ -3,5 +3,5 @@ Minimization: step4.in imin = 1, ntmin = 2, maxcyc = 1000, ncyc = 10, ntwx = 500, ioutfm = 1, ntxo = 2, ntpr = 50, ntwr = 500, ntc = 1, ntf = 1, ntb = 1, cut = 8.0, - ntr = 1, restraintmask = ":1-5&!@H=,:8-13&!@H=", restraint_wt = 0.1, + ntr = 1, restraintmask = ":1-5&!@H=|:8-13&!@H=", restraint_wt = 0.1, &end diff --git a/test/modified.residues/Save/step6.in b/test/modified.residues/Save/step6.in index 92f0fdd..c4388e5 100644 --- a/test/modified.residues/Save/step6.in +++ b/test/modified.residues/Save/step6.in @@ -7,5 +7,5 @@ MD: step6.in ntc = 2, ntf = 2, ntb = 2, cut = 8.0, ntt = 3, gamma_ln = 5, temp0 = 300, tempi = 300, ntp = 1, barostat = 2, pres0 = 1.0, mcbarint = 100, - ntr = 1, restraintmask = ":1-5&!@H=,:8-13&!@H=", restraint_wt = 1.0, + ntr = 1, restraintmask = ":1-5&!@H=|:8-13&!@H=", restraint_wt = 1.0, &end diff --git a/test/modified.residues/Save/step7.in b/test/modified.residues/Save/step7.in index dcc2d16..0e97c91 100644 --- a/test/modified.residues/Save/step7.in +++ b/test/modified.residues/Save/step7.in @@ -7,5 +7,5 @@ MD: step7.in ntc = 2, ntf = 2, ntb = 2, cut = 8.0, ntt = 3, gamma_ln = 5, temp0 = 300, tempi = 300, ntp = 1, barostat = 2, pres0 = 1.0, mcbarint = 100, - ntr = 1, restraintmask = ":1-5&!@H=,:8-13&!@H=", restraint_wt = 0.5, + ntr = 1, restraintmask = ":1-5&!@H=|:8-13&!@H=", restraint_wt = 0.5, &end diff --git a/test/modified.residues/Save/step8.in b/test/modified.residues/Save/step8.in index 651e9a4..b11e8db 100644 --- a/test/modified.residues/Save/step8.in +++ b/test/modified.residues/Save/step8.in @@ -7,5 +7,5 @@ MD: step8.in ntc = 2, ntf = 2, ntb = 2, cut = 8.0, ntt = 3, gamma_ln = 5, temp0 = 300, tempi = 300, ntp = 1, barostat = 2, pres0 = 1.0, mcbarint = 100, - ntr = 1, restraintmask = ":1-5@H,N,CA,HA,C,O,:8-13@H,N,CA,HA,C,O", restraint_wt = 0.5, + ntr = 1, restraintmask = ":1-5@H,N,CA,HA,C,O|:8-13@H,N,CA,HA,C,O", restraint_wt = 0.5, &end diff --git a/test/modified.residues/test.out.save b/test/modified.residues/test.out.save index 27d2976..01bb857 100644 --- a/test/modified.residues/test.out.save +++ b/test/modified.residues/test.out.save @@ -6,8 +6,8 @@ AmberMdPrep.sh Version 0.6 (beta) Warning: Unknown residues detected; will be ignored for restraints. Detected types : protein NUM SOLUTE RES : 11 - HEAVY MASK : :1-5&!@H=,:8-13&!@H= - BACKBONE MASK : :1-5@H,N,CA,HA,C,O,:8-13@H,N,CA,HA,C,O + HEAVY MASK : :1-5&!@H=|:8-13&!@H= + BACKBONE MASK : :1-5@H,N,CA,HA,C,O|:8-13@H,N,CA,HA,C,O TEMPERATURE : 300 OVERWRITE : 0 MD COMMAND : pmemd From 62e75a9654b57c4565638aaf604945337a111274 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Fri, 6 Feb 2026 10:05:36 -0500 Subject: [PATCH 3/3] v0.7b. Minor bump for fixed mask expression --- AmberMdPrep.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AmberMdPrep.sh b/AmberMdPrep.sh index db05696..c5ae53f 100755 --- a/AmberMdPrep.sh +++ b/AmberMdPrep.sh @@ -6,7 +6,7 @@ # NIH/NHLBI # 2020-08-07 -VERSION='0.6 (beta)' +VERSION='0.7 (beta)' MPIRUN=`which mpirun` CPPTRAJ=`which cpptraj`