对于原子坐标不一致这个问题，我也遇到过。对于不想重新top、crd的解决办法是：你用来计算的那个化合物（包含配体和蛋白质的），把配体的原子信息复制粘贴出来重新做成pdb文件，再保存crd和top文件，希望这条信息对你有用。
2012/10/29 Yulin Huang <yulinhuang2007.gmail.com>
> Dear Amber users:
> I am performing binding free energy calculation for a kinase with
> 12 ligands using thermodynamic integration (AMBER11). It seems that the
> atom names and orders for the corresponding atoms in these 12 ligands in
> the initial setup have to be the same. Thus the
> parm files and crd files generated after I use the antechamber, parmchk
> could be the same
> for the corresponding atoms. After that, the small mask (one or two atoms)
> can be specified for calculations.
>
> I have manually made all the corresponding atom names the same. Now I am
> trying to make the order the same. It is not an easy task. The way I do is
> to put all the different atoms among 12 ligands at the end of ligand mol2
> files. But I have to change all the connectivity part. I've tried to load
> the mol2 file into software MOE and output the pdb file and then convert to
> mol2 file. But the different atom such as O will be placed in the middle
> of the mol2 file automatically. But I have to put the different atoms in
> the end to make the corresponding atoms in the same order.
>
> Does anyone has any ideas for this problems? Many thanks in advance.
>
> --
> Yulin "Joyce" Huang
> Ph.D Candidate
> Computational Chemistry (CADD)
> Advisor: Dr. Robert C. Rizzo
> State University of New York at Stony Brook
> Stony Brook NY,11790
> Office: (631)632-8519
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Received on Mon Oct 29 2012 - 08:00:06 PDT
