Dear AMBER user and Developer,
I have cpptraj with version 13.0. I read a comment from Daniel Roe that
right now the version of cpptraj is 13.22.
I'd like to know how to update my cpptraj.
That is my first question.
Second question,
I'd like to set donor an acceptor mask for hbond calculation like this :
==========
donor mask ".O,OXT"
donor mask ":ASP.OD1,OD2"
donor mask ":GLU.OE1,OE2"
donor mask ":ASN.OD1"
donor mask ":GLN.OE1"
donor mask ":SER.OG"
donor mask ":THR.OG1"
donor mask ":TYR.OH"
donor mask ":ASN.ND2"
donor mask ":GLN.NE2"
donor mask ":HIE.ND1"
donor mask ":HID.NE2"
acceptor mask "!:PRO & !:1 & .N" ".H"
acceptor mask ":1 & .N" ":1 & .H1"
acceptor mask ":1 & .N" ":1 & .H2"
acceptor mask ":1 & .N" ":1 & .H3"
acceptor mask ":LYS & .NZ" ":LYS & .HZ1"
acceptor mask ":LYS & .NZ" ":LYS & .HZ2"
acceptor mask ":LYS & .NZ" ":LYS & .HZ3"
acceptor mask ":ARG & .NH1" ":ARG & .HH11"
acceptor mask ":ARG & .NH1" ":ARG & .HH12"
acceptor mask ":ARG & .NH2" ":ARG & .HH21"
acceptor mask ":ARG & .NH2" ":ARG & .HH22"
acceptor mask ":ARG & .NE" ":ARG & .HE"
acceptor mask ":HIP & .NE2" ":HIP & .HE2"
acceptor mask ":HIP & .ND1" ":HIP & .HD1"
acceptor mask ":HIE & .NE2" ":HIE & .HE2"
acceptor mask ":HID & .ND1" ":HID & .HD1"
acceptor mask ":SER & .OG" ":SER & .HG"
acceptor mask ":THR & .OG1" ":THR & .HG1"
acceptor mask ":TYR.OH" ":TYR.HH"
acceptor mask ":TRP.NE1" ":TRP.HE1"
acceptor mask ":GLN.NE2" ":GLN.HE21"
acceptor mask ":GLN.NE2" ":GLN.HE22"
acceptor mask ":ASN.ND2" ":ASN.HD21"
acceptor mask ":ASN.ND2" ":ASN.HD22"
==================
I got this from tutorial, but this mask was used with ptraj.
Would somebody help me how to set up donor and acceptor mask like above ?
Thank you very much
Setyanto Tri Wahyudi
Institut Teknologi Bandung
Program Studi Kimia
Lab Biokimia
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Received on Wed Mar 26 2014 - 02:00:02 PDT
