Dear Amber users,
I am wondering how PMEMD handle duplicates in GROUP definitions, do they
get added together or overwritten?
I want to use 2 different restraint forces for the side chain and the
backbone of a protein.
I define the 2 groups as follow. My goal is to have a force constant of 10
for the backbone and 5 for side chain. Is this the correct way to do that
or do I need to spell out all atoms of the side chain? I am using
Charmm-gui output so I can't group based on tree name.
Thank you!
Protein SC posres
5.0
RES 1 297
END
Protein BB posres
5.0
FIND
CA * * *
C * * *
O * * *
N * * *
SEARCH
RES 1 297
END
the mdout file gives:
----- READING GROUP 1; TITLE:
Protein SC posres
GROUP 1 HAS HARMONIC CONSTRAINTS 5.00000
GRP 1 RES 1 TO 297
Number of atoms in this group = 4887
----- READING GROUP 2; TITLE:
Protein BB posres
GROUP 2 HAS HARMONIC CONSTRAINTS 5.00000
ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE
INCLUDED IN GROUP BELOW
GRAPH NAME = CA SYMBOL = * TREE SYMBOL = * RESIDUE TYPE
= *
GRAPH NAME = C SYMBOL = * TREE SYMBOL = * RESIDUE TYPE
= *
GRAPH NAME = O SYMBOL = * TREE SYMBOL = * RESIDUE TYPE
= *
GRAPH NAME = N SYMBOL = * TREE SYMBOL = * RESIDUE TYPE
= *
GRP 2 RES 1 TO 297
Number of atoms in this group = 1184
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Received on Mon Aug 19 2019 - 12:30:02 PDT
