Dear all,
I am working on a DNA-RNA hybrid structure. While I load my pdb structure
using the following combination, I get the error:
source leaprc.water.tip3p
source leaprc.DNA.bsc1
source leaprc.RNA.OL3
loadoff terminal_monophosphate.lib
nuc=loadpdb nuc.pdb
saveamberparm nuc nuc.prmtop nuc.inpcrd
####
Error: For atom (.R<DC5 31>.A<C5' 7>) could not find vdW (or other)
parameters for type (CJ)
Error: For atom (.R<DC5 31>.A<C3' 30>) could not find vdW (or other)
parameters for type (C7)
Error: For atom (.R<DC5 85>.A<C5' 7>) could not find vdW (or other)
parameters for type (CJ)
Error: For atom (.R<DC5 85>.A<C3' 30>) could not find vdW (or other)
parameters for type (C7)
Warning: Parameter file was not saved.
####
However, when I use the OL15 parameters, I do not get this error. Could
someone please suggest what might be the problem?
Any help would be appreciated.
Regards,
Sruthi
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Received on Fri Jun 13 2025 - 12:00:02 PDT
