VMD-L Mailing List
From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Jan 08 2016 - 13:57:47 CST
>From the solvate manual page:
Beginning in VMD 1.8.6, it is possible to solvate a system with solvents other than water. In order to do this, you must prepare:
â€¢ An equilibrated, cubic box of the solvent of choice (-spdb)
â€¢ A psf file for the solvent cube (-spsf)
â€¢ A topology file for all residue types in the solvent (-stop)
â€¢ A key selection which will occur once in each solvent residue (eg., "name OH2") (-ks) **
â€¢ The side length of the box (should be taken from the equilibration's periodic cell (-ts)
These five items are the **required** inputs for using an alternative solvent; if they are not specified (on the command line) or changed (in the GUI) standard TIP3P water will be used. To use an alternate solvent in the command line mode, **specify the five required inputs for solvate using the flags listed above**. **Please note that your solvent pdb must have segid QQQ for all atoms**. In addition, all solvent residues should be in the same chain and each residue should have a unique resid (ie, for mixed solvents, do not use separate residue numbering schemes for the multiple solvent types.
Iâ€™ve taken the liberty of starring several key sections of this documentation. We can tweak the command line help to make this clearer, but in general such help texts are a supplement, not replacement, for the real documentation.
Regarding the segname overflow, can you send an exact example so I can reproduce it?
> On Jan 6, 2016, at 4:27 AM, Vlastimil ZÃma <zima_at_karlov.mff.cuni.cz> wrote:
> Hi everybody,
> I believe I found several bugs in solvate plugin when I tried to use it with custom solvent.
> * Custom solvent has to have a segment QQQ otherwise it doesn't work and it is very hard to find where the problem is.
> * All arguments for custom solvent are required, but than is neither stated not validated when using command line. This causes errors which are hard to debug.
> * Solvate plugin is able to generate invalid segnames, longer than 4 chars, if the is really large copies of the solvent.
> * Values for -ks argument are required to be selections, not the names of the atoms as suggested by the help.
> I hope at least some of the issues will be addressed.