AMBER Archive (2008)

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

From: Grange Hermitage (ghermitage_at_gmail.com)
Date: Sun Aug 17 2008 - 21:28:17 CDT

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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