[AMBER] Failed to merge the protein-ligand amoeba parameters

From: 王茜茜 <wangqq430.gmail.com>
Date: Tue, 27 Nov 2018 16:46:01 +0800

Dear developers,
     Recently, I want to test the polariable-force-field simulation for a
protein-ligand complex. Using Poltype, I obtained the lig.key and lig.xyz.
Using tinker_to_amber, I obtained the prot_solv.prmtop, prot_solv.inpcrd,
prot_solv.key and prot_solv.xyz (with amoebapro13). Importantly, both of
them works well by checking "analyze X.xyz -k X.key ep".
    To build com_solv.prmtop and com_sol.inpcrd, I further merged the .xyz
files of protein and ligand using "xyzedit", and meanwhile append the
lig.key into prot.key to obtain the com.key. But when checking "analyze
com.xyz -k com.key ep", it gave the wrong information below:
 MECHANIC -- Some Required Potential Energy Parameters are Undefined

 TINKER is Unable to Continue; Terminating the Current Calculation
    Maybe it's the problem of com.key, but the tutorial told to just append
the prot.key into lig.key. I donnot know how to solve it. And to build the
complex system, whether what I did are right or not? Any reply will be
grateful. Thank you.





Best regards!


Qianqian
Macau university of science and technology


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Received on Tue Nov 27 2018 - 01:00:02 PST
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