Hi Jason,<br/> Thank you very much. My question was solved based on your suggestion!<br/>Best wish.
At 2014-05-30 09:30:13, "Jason Swails" <jason.swails.gmail.com> wrote:
>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 Sat May 31 2014 - 01:00:02 PDT
