From: ZOU Changling (zoucl_at_ihep.ac.cn)
Date: Wed May 27 2015 - 04:31:28 CDT
I have a problem when i use Replica exchange to research my protein.I can't submit my task because my parameters about protein have some errors about format, like following:
Redirecting stdout to files /vol-th/home/nanocas/zoucl/lib1/replica/example/output/0/job0.0.log through 7
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CT1 And the next is the relevants in my parameter:
NONBonded H 0.0498 1.4254 0.0498 1.4254
NONBonded HA 0.0450 2.6157 0.0450 2.6157 !- charged group.
NONBonded HC 0.0498 1.0691 0.0498 1.0691 ! Reduced vdw radius
!
NONBonded C 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon
NONBonded CH1E 0.0486 4.2140 0.1000 3.3854 ! \
NONBonded CH2E 0.1142 3.9823 0.1000 3.3854 ! extended carbons
NONBonded CH3E 0.1811 3.8576 0.1000 3.3854 ! /
! NONBonded CM 0.0262 4.4367 0.1000 3.3854
NONBonded CR1E 0.1200 3.7418 0.1000 3.3854 ! ring carbons
! NONBonded CT 0.0262 4.4367 0.1000 3.3854
NONBonded CT1 -0.0200 2.2750 -0.0100 1.9000 ! ALLOW ALI
NONBonded CT2 -0.0550 2.1750 -0.0100 1.9000 ! ALLOW ALI
NONBonded CT3 -0.0800 2.0600 -0.0100 1.9000 ! ALLOW ALI
NONBonded CT -0.0200 2.275 -0.0100 1.9000 ! from CT1x: needs work
NONBonded CT1x -0.0200 2.275 -0.0100 1.9000 ! alkane, 3/92: needs work
NONBonded CT2x -0.0560 2.010 -0.0100 1.9000 ! alkane, 4/98, yin, adm jr.
NONBonded CT3x -0.0780 2.040 -0.0100 1.9000 ! alkane, 4/98, yin, adm jr.
NONBonded N 0.2384 2.8509 0.2384 2.8509
NONBonded NC2 0.2384 2.8509 0.2384 2.8509
NONBonded NH1 0.2384 2.8509 0.2384 2.8509
NONBonded NH2 0.2384 2.8509 0.2384 2.8509
As you can see the green word has shown the CT1,so why it give me the error?
I am looking forward to your answer and reply!
Thank you!
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