AMBER Archive (2009)

Subject: Re: [AMBER] crystal waters

From: steinbrt_at_rci.rutgers.edu
Date: Mon Jan 12 2009 - 14:16:25 CST

Hi Carmen,

not sure if that might be the cause, but does your input pdb contain water
hydrogens? Does your output look better when you delete them and have leap
re-add them to your system? I would normally expect X-ray crystal waters
to only have the oxygen position resolved, but I dont know where your pdb
comes from...

Regards,

Thomas

On Mon, January 12, 2009 3:04 pm, Carmen Domene wrote:
>
> 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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> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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