Hi Jason,
Thank you for your reply. I want to protonate the N3 of the base of cytosine 6 in my nucleic 1zih. it can protonate the N3 of the cytosine 6. But when i save the parameter of the force field using the command saveamberparm, it occures error. the error is following:
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
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!
At 2014-05-28 11:12:39, "Jason Swails" <jason.swails.gmail.com> wrote:
>On Wed, May 28, 2014 at 10:56 AM, 王珍 <wangzhenzk.126.com> wrote:
>
>> Hi Jason,I want to protonate the N3 of the base of the nucleic CYT 62.
>> After i loadoff the all_pronate_nucleic10.lib, but i can not save the
>> parameter force field use the saveamberparm. the error is : For atom: R<CP
>> 62>. A <C6 14> could not find type; C1
>>
>> For atom: R<CP 62>. A <C5
>> 16> could not find type; C1
>> Parameter file was not
>> saved.
>> when i use the loadAmberParams frcmod.protonated_nucleic, the error is
>> same.
>>
>
>There is not enough information here. The C5 atom of the CP residue has
>type C4, not C1. So with the context you have provided this error does not
>make sense to me. You need to tell us everything you actually did (full
>input files with full output files, as well as any other relevant details
>about your setup).
>
>--
>Jason M. Swails
>BioMaPS,
>Rutgers University
>Postdoctoral Researcher
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- application/octet-stream attachment: 1zih.pdb
Received on Wed May 28 2014 - 18:30:02 PDT
