Hi Sir,
I want to protonate the N3 of the base of cytosine 6 in my nucleic 1zih. But when i save the parameter of the force field using the command saveamberparm, it occures error. the error is following:
Building topology.
Building atom parameters.
For atom: R<CP 6>. A <C6 14> could not find type; C1
For atom: R<CP 6>. A <C5 16> could not find type; C1
Parameter file was not saved.
<<The process I used is following:
reduce 1zih.pdb > 1.pdb
tleap -s -f leaprc.ff99bsc0
loadoff /home/d/AmberTools12/amber12/dat/leap/lib/all_prot_nucleic10.lib/
loadAmberParams frcmod.protonated_nucleic
r1=loadpdb 1.pdb
saveamberparm r1 r1.top r1.crd>>
Thank you very much!
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- application/octet-stream attachment: 1zih.pdb
Received on Thu May 29 2014 - 18:00:02 PDT
