Dear amber users,
I am trying to do an umbrella sampling, and as long as I follow the
tutorial(
http://ambermd.org/tutorials/advanced/tutorial17/section1.htm )
for restraining the dihedrals everything goes well.
However, when restraining a distance with
$AMBERHOME$/makeDIST -upb 7col.dist -pdb temp.pdb -rst RST.dist
I get the following error
"
ERROR no map function for HH31 ACE :data= 1 ACE HH31 1 ACE CHE3 2.0 "
Note, I converted one of files(ala_tri.inpcrd) to temp.pdb , and here is
the head of this latter
CRYST1 34.759 34.759 34.759 109.47 109.47 109.47 P 1 1
ATOM 1 HH31 ACE X 1 20.815 15.054 12.824 0.00 0.00
H
ATOM 2 CH3 ACE X 1 20.164 15.871 13.133 0.00 0.00
C
ATOM 3 HH32 ACE X 1 19.266 15.875 12.515 0.00 0.00
H
ATOM 4 HH33 ACE X 1 20.689 16.819 13.017 0.00 0.00
H
ATOM 5 C ACE X 1 19.747 15.720 14.598 0.00 0.00
C
ATOM 6 O ACE X 1 20.145 14.767 15.264 0.00 0.00
O
ATOM 7 N ALA X 2 18.946 16.666 15.092 0.00 0.00
N
ATOM 8 H ALA X 2 18.645 17.431 14.505 0.00 0.00
--
whilst I am using this 7col.dist
1 ACE HH31 1 ACE CHE3 2.0 # comments go here
So, here I am trying to restrain the distance between the first two atoms
in the temp.pdb file ( the choice is just for testing makeDIST).
Does anybody know how to get it right?
Cheers,
*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Mon Oct 08 2018 - 07:30:03 PDT
