AMBER Archive (2008)

Subject: Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro

From: Grange Hermitage (ghermitage_at_gmail.com)
Date: Mon Aug 18 2008 - 00:04:18 CDT

The definition of the water model is hardcoded in amb2gmx.pl

On Mon, Aug 18, 2008 at 11:58 AM, Grange Hermitage <ghermitage_at_gmail.com>wrote:

> Hi all,
>
> when the following leap script (AmberTools 1.2) is executed and followed by
> amb2gmx.pl, the .top file is suitable for TIP3P and the .gro is suitable for
> TIP4PEW. The .top file knows nothing about EPW. Gromacs then remarks that
> the nunber of atoms in the .top and .gro don't match. Is there something
> amiss in the leap file? There are no waters in chp16.pdb .
>
> Thanks,
> John.
>
>
> source leaprc.ff99SB
> WAT = T4E
> set WAT.1 name "T4E"
> loadamberparams frcmod.tip4pew
> loadoff ions94.lib
> loadamberparams frcmod.ionsjc_tip4pew
> loadoff chk.lib
> loadoff chd.lib
> chp16 = loadpdb chp16.pdb
> check chp16
> solvatebox chp16 TIP4PEWBOX 5 iso
> addions chp16 Na+ 17
> addions chp16 Cl- 13
> check chp16
> saveamberparm chp16 chp16leap.prm chp16leap.crd
> quit
>
>

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