What OS are you using and how was VMD installed?
// Gustaf
> On 23 May 2018, at 05:43, Karla Galdamez <kmgaldam.ucsc.edu> wrote:
>
> Hello,
>
> I hope you are well! I am trying to activate a VMD window to reformat a
> restart.rst file, would anyone share how to bring forth the VMD window from
> the command line?
>
> Thank you!
> Karla
>
> On Tue, May 22, 2018 at 5:32 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Tue, May 22, 2018, Sadegh Faramarzi Ganjabad wrote:
>>>
>>> Thanks for replying. Those atoms are actually parts of a water molecule.
>>> That's why I'm surprised, if AMBER allows an H-H bond why it gives that
>>> error? Can't it be because in the original psf file those extra bonds
>>> already exist?
>>
>> We need more information, as I mentioned earlier: how exactly did you
>> convert CHARMM to Amber format, and what version of AmberTools are you
>> using? (Problems with waters in earlier versions have been fixed.)
>>
>> ....dac
>>
>>
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>
>
>
> --
> Karla M. Galdamez, Ph.D
> Research Fellow
> Chemistry and Biochemistry Department
> kmgaldam.ucsc.edu
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Received on Tue May 22 2018 - 23:30:01 PDT
