VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Feb 14 2014 - 12:41:36 CST

One additional detail: the psf/pdb pair should have the solvent's
segname set to "QQQ".
-Josh Vermaas

On 2/14/14, 9:23 AM, Tim Lo wrote:
> Hi Javad,
>
> Please be careful of the shape of the solvent box too. The
> pre-equilibrated box should be cubic in order for VMD Solvate to run
> properly. When you perform equilibration of your solvent box, you
> should set the three cell basis vectors of the Periodic Boundary
> Conditions to be the same.
>
> Regards,
> Tim
>
> On 2014/2/14 ?? 08:47, Norman Geist wrote:
>>
>> VMDs solvate GUI is able to handle non standard solvent. All you need
>> is a pre-equilibrated box with pdb/psf and its topology.
>>
>> Norman Geist.
>>
>> *Von:*owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>> Auftrag von *Javad Noroozi
>> *Gesendet:* Freitag, 14. Februar 2014 12:59
>> *An:* namd-l_at_ks.uiuc.edu
>> *Betreff:* namd-l: Solvation in non standard solvent
>>
>> How can solvate a drug in non standard solvent using NAMD?
>>
>> Javad Noroozi
>>
>> Chemical Engineering Department
>>
>> Sharif University of Technology
>>
>> Email: jnoroozi_at_che.sharif.ir <mailto:jnoroozi_at_che.sharif.ir>
>>
>>
>>
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>