On Fri, 2014-05-30 at 08:45 +0800, 王珍 wrote:
> 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
I have no idea how you are getting this error message. When I run your
example, the error message says the type that could not be found was C4,
not 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>>
Your problem is that you are using ff99bsc0, which is quite old at this
point. The atom typing in the protonated nucleic acid library is
incompatible with the standard ff99bsc0 atom typing.
Use a more modern force field instead, like ff14SB. See the third
chapter of the Amber 14 manual for details about the different force
fields.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 30 2014 - 07:00:03 PDT
