Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization

From: 张冬冬 <>
Date: Fri, 22 Aug 2014 22:56:01 +0800 (GMT+08:00)

Thanks very much for your suggestions last time. Now that problem has been solved. Many thanks.
At present, I have a new question emerging on my test of running minimization using a restraint file. The restraint file is regarded to four distance restraints between some atoms. After every minimization, I observed the results in the VMD, checking the four distances defined in the restraint file. In the step three of minimization, the four distances group in the restraint file, however, turned to be above the defined upper distance, which should not happen in this situation. On the other hand, in the MD step, by observing another test, I find that the distances group in the restraint file are strongly met with distance range, neither below the lower distance nor above the upper distance. So, I wonder that, whether the restraint file is not effective in the minimization. Thank you!

> -----原始邮件-----
> 发件人: "David A Case" <>
> 发送时间: 2014年8月15日 星期五
> 收件人: "AMBER Mailing List" <>
> 抄送:
> 主题: Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization
> On Fri, Aug 15, 2014, 张冬冬 wrote:
> > Actually I'm quite sure about the underlying problem behind the results,
> > which have large RMS, stars form like **** of VDW and EEL in it. I
> > have checked the system structure and found that there are two atoms (
> > belonging to different residues ) getting very closer (almost sitting
> > on each other) and one near bond is stretched after finishing the
> > minimization step two.
> A wild guess: are you using SHAKE for hydrogens? You need to do this for
> most Amber force fields. Beyond that, you'll have to try to figure out what
> is going on with the atoms involved in the bad contact. It is possible that
> you are getting a "polarization catastrophe" where two induced dipoles get too
> close together. I don't have much experience with ff02 myself.
> ...dac
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Received on Fri Aug 22 2014 - 08:00:03 PDT
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