Dear Amber Users,
I get the following warning message when I load the topology file into VMD.
I checked the bond and in xleap this does not show any such message . Can
you tell me is this a
issue with my starting structures.
Warning) Unusual bond between residues: 71 (protein) and 72 (none)
Warning) Unusual bond between residues: 73 (protein) and 74 (none)
Warning) Unusual bond between residues: 75 (protein) and 76 (none)
Warning) Unusual bond between residues: 77 (protein) and 78 (none)
Warning) Unusual bond between residues: 79 (protein) and 80 (none)
Warning) Unusual bond between residues: 81 (protein) and 82 (none)
Warning) Unusual bond between residues: 83 (protein) and 84 (none)
Warning) Unusual bond between residues: 85 (protein) and 86 (none)
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 21000 TIME(PS) = 221.000 TEMP(K) = 308.48 PRESS =
0.0
Etot = 4704.1640 EKtot = 2825.6846 EPtot =
1878.4794
BOND = 1084.4094 ANGLE = 1313.6891 DIHED =
776.0708
1-4 NB = 578.7901 1-4 EEL = -352.6533 VDWAALS =
-1128.1578
EELEC = -393.6689 EGB = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Thanks
Kirtana
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Received on Tue May 08 2012 - 07:30:04 PDT
