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Re: about reading frame from dcd one by one
rmv #27463 05/10/11 09:29 PM
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zzlai Offline OP
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should I run the simulation again? Or is there any method to change the current coordinates?

Re: about reading frame from dcd one by one
zzlai #27464 05/10/11 09:37 PM
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traj read
coor orient
write coor pdb name xxxx.pdb

You have clearly demonstrated that you know just a little of how CHARMM works, so how do you know that CHARMM cannot do the analysis that you want to do?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: about reading frame from dcd one by one
lennart #27465 05/10/11 10:23 PM
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zzlai Offline OP
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:)thanks for your help!
I am a beginner of CHARMM. Before I always use AMBER. Exactly because I know very little of how CHARMM works, I don't know whether CHARMM can or cannot do the analysis that I want. I never doubt CHARMM is very powerful,even if it is sort of difficult for the beginner. smile

Anyway, I learned quite a few things from this. Learning needs some time. smile

I have another question. Now I would like to simulate a system with nonstandard residues. How should I create their topology and parameter files? Do I need the quantum calculation or just modify the specific part in the rtf file? thanks!

Last edited by zzlai; 05/10/11 10:24 PM.
Re: about reading frame from dcd one by one
zzlai #27466 05/10/11 10:30 PM
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See the posts for CGenFF and related topics in the Parameters forum. What needs to be done may be different for each molecule, depending on how closely related it is to existing residues.


Rick Venable
computational chemist

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