From: Joseph Heil (jpheil_at_ncsu.edu)
Date: Mon Nov 19 2007 - 22:00:57 CST
I am using the psfgen NAMD extension in VMD to try and generate a psf
file for ammonia. I get the error: Warning: failed to set coordinate
for atom 1H MOL:1 U
same problem for the other 2 hyrdogens but not for nitrogen
so I think the error is in my pdb file.
pdb file:
! 1 2 3
4 5 6 7
!2345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 1 N MOL U 1 0.000
0.000 0.000 1.00 0.00 N
ATOM 2 1H MOL U 1 -0.000
0.363 1.028 1.00 0.00 H
ATOM 3 2H MOL U 1 -0.890
0.363 -0.514 1.00 0.00 H
ATOM 4 3H MOL U 1 0.890
0.363 -0.514 1.00 0.00 H
END
topology file:
! 1 2 3 4
!23456789012345689012345678901234567890
MASS 1 N1 14.01 N
MASS 2 H1 01.008 H
!DEFA FIRS NTER LAST CTER
!AUTO ANGLES DIHE
! 1 2 3 4
!23456789012345689012345678901234567890
RESI MOL 0.00
GROUP
ATOM N N1 -.600
ATOM 1H H1 +0.200
ATOM 2H H1 +0.200
ATOM 3H H1 +0.200
BOND N 1H N 2H N 3H
DEFA FIRS NTER LAST CTER
AUTO ANGLES DIHE
PATCHING FIRS NONE LAST NONE
any suggestions on what to change or knowledge on space dependent
formatting of topology files would be greatly appreciated.
Thank you,
Joseph Heil
NC State University
College of Textiles
Textile Engineering Chemistry and Science
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