From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue May 01 2012 - 11:34:48 CDT
Please post the script or no one can help you.
Ideally, if you could make all your input and output files available on the web for download, it would be easier to see what's going on.
On May 1, 2012, at 11:18 AM, Raghav wrote:
> It is the usual psfgen with vmd using top_all27_protein_lipid_na.top.
>
> On May 1, 2012, at 17:48, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>
>> Post the psfgen script you're using to build your system so that someone can hopefully identify what you're doing wrong.
>>
>> On Apr 30, 2012, at 4:55 AM, raghav singh wrote:
>>
>>> Hi All,
>>>
>>> I have a question about total charge of nucleic acid system... no matter what I have tried it does not sum up to an integer value... for a double stranded helix of 24 bp ...i is like 45.9999 ......!! something like this (with terminal patch).
>>> during ionization it tells me that I have to add 46 ions to neutralize the system... but it come up with some positive value?
>>>
>>> while if I understand it right it should be -48 with terminal patch or -47 with terminal patch. (gromacs, amber ).
>>>
>>> and after solvation and ionization it comes up with some positive value of 1.23446 ... !!
>>>
>>> if someone have any idea abt it.. please tell me how can solve this one.
>>>
>>> Thank You
>>>
>>> Raghav
>>>
>>>
>>
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