From f51fb888d86c84de3a161191b9b704ebd80066d8 Mon Sep 17 00:00:00 2001 From: andrea-arsiccio Date: Sat, 26 Jun 2021 16:55:27 +0200 Subject: [PATCH] try to make sasa appear under module --- regtest/sasa/Makefile | 2 ++ src/sasa/sasa_HASEL.cpp | 5 +++-- src/sasa/sasa_LCPO.cpp | 5 +++-- user-doc/spelling_words.dict | 2 ++ 4 files changed, 10 insertions(+), 4 deletions(-) create mode 100644 regtest/sasa/Makefile diff --git a/regtest/sasa/Makefile b/regtest/sasa/Makefile new file mode 100644 index 0000000000..42480767ae --- /dev/null +++ b/regtest/sasa/Makefile @@ -0,0 +1,2 @@ +include ../scripts/module.make + diff --git a/src/sasa/sasa_HASEL.cpp b/src/sasa/sasa_HASEL.cpp index b175dcf404..825caeb882 100644 --- a/src/sasa/sasa_HASEL.cpp +++ b/src/sasa/sasa_HASEL.cpp @@ -43,9 +43,10 @@ namespace sasa { Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The algorithm described in \cite Hasel1988 is used for the calculation. The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of SASA is updated (the default is every 10 steps). Different properties can be calculated and selected using the TYPE keyword: -the total SASA (TOTAL); -the free energy of transfer for the protein according to the transfer model (TRANSFER. This keyword can be used, for instance, to compute the transfer of a protein to different temperatures, as detailed in \cite Arsiccio-SASA-2021). +1) the total SASA (TOTAL); + +2) the free energy of transfer for the protein according to the transfer model (TRANSFER. This keyword can be used, for instance, to compute the transfer of a protein to different temperatures, as detailed in \cite Arsiccio-SASA-2021). When the TRANSFER keyword is used, a file with the free energy of transfer values for the sidechains and backbone atoms should be provided (using the keyword DELTAGFILE). Such file should have the following format: diff --git a/src/sasa/sasa_LCPO.cpp b/src/sasa/sasa_LCPO.cpp index bcdc209e51..d840639b91 100755 --- a/src/sasa/sasa_LCPO.cpp +++ b/src/sasa/sasa_LCPO.cpp @@ -43,9 +43,10 @@ namespace sasa { Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The LCPO algorithm is used for the calculation (please, read and cite \cite Weiser1999). The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of the SASA is updated (the default is every 10 steps). Different properties can be calculated and selected using the TYPE keyword: -the total SASA (TOTAL); -the free energy of transfer for the protein according to the transfer model (TRANSFER. This keyword can be used to compute the transfer of a protein to different temperatures, as detailed in \cite Arsiccio-SASA-2021). +1) the total SASA (TOTAL); + +2) the free energy of transfer for the protein according to the transfer model (TRANSFER. This keyword can be used to compute the transfer of a protein to different temperatures, as detailed in \cite Arsiccio-SASA-2021). When the TRANSFER keyword is used, a file with the free energy of transfer values for the sidechains and backbone atoms should be provided (using the keyword DELTAGFILE). Such file should have the following format: diff --git a/user-doc/spelling_words.dict b/user-doc/spelling_words.dict index d7d70ad669..c6a4ebbdde 100644 --- a/user-doc/spelling_words.dict +++ b/user-doc/spelling_words.dict @@ -360,6 +360,7 @@ gyromagnetic GSL CRYST piv +sasa namespaces OSX libplumedKernel @@ -906,6 +907,7 @@ AFED LogPD LOGMFDMOD PIVMOD +SASAMOD logmfd MFD adiabatically