AMBER Archive (2009)

Subject: [AMBER] crystal waters

From: Carmen Domene (carmen.domene_at_chem.ox.ac.uk)
Date: Mon Jan 12 2009 - 14:04:24 CST

Hi.

I have been checking in the amber repository but I have not found a
solution to my problem. I am trying to generate the topology file for a
system composed of a protein, a ligand and some crystal waters. I would
also like to solvate it and add counter ions.

I am using this set of commands:

tleap -s -f leaprc.ff99SB
source leaprc.gaff
loadamberprep p.prepin
loadamberparams p.frcmod
LIG=loadpdb all_1.pdb
check LIG
solvateBOX LIG TIP3PBOX 11
addions LIG Na+ 0
center LIG
>The center is at: 0.27, 0.14, -0.09
translate LIG {-0.27, -0.14, 0.09}
center LIG
>The center is at: 0.00, -0.00, -0.00
savepdb LIG all_c.pdb
LIG2=loadpdb all_c.pdb
saveamberparm LIG2 all_c.prmtop all_c.inpcrd

I am using Amber9.

What I find is that the crystal waters and the waters
added by the solvation procedure have the atoms organised
in different ways, for example 832 is a crystal water
and 833 is a water added during solvation:

TER
ATOM 7774 H1 WAT 832 -32.473 -7.620 7.472 1.00 0.00
ATOM 7775 H2 WAT 832 -33.670 -6.694 7.472 1.00 0.00
ATOM 7776 O WAT 832 -33.430 -7.620 7.472 1.00 0.00
TER
ATOM 7777 O WAT 833 41.569 48.050 38.824 1.00 0.00
ATOM 7778 H1 WAT 833 40.737 47.794 39.224 1.00 0.00
ATOM 7779 H2 WAT 833 42.177 48.121 39.560 1.00 0.00
TER

When I run the MD I can see the crystal waters look wrong with d_O-H1
different from d_O-H2.

What should I do to have the atoms in the same order in all the water
molecules?

I have tried using HOH rather than WAT or the other way round. Adding
'TER' after each O of the crystal waters...

Thanks,

Carmen

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