Dear Carlos,
Thank you very much for your reply.
And I am sorry not to explain my modified topology file.
(But didn't you receive the attached file in the previous E-mail?
Does AMBER-mailing-list not send the attached file?)
O.K., I will explain here.
"Original" topology file is from PDB file below, by Leap module.
---------wat2.pdb------------------------------------
REMARK TP3
ATOM 1 O WAT 1 0.000 0.000 0.000
ATOM 2 H1 WAT 1 0.957 0.000 0.000
ATOM 3 H2 WAT 1 -0.240 0.927 0.000
TER
ATOM 1 O WAT 2 0.000 0.000 4.000
ATOM 2 H1 WAT 2 0.957 0.000 4.000
ATOM 3 H2 WAT 2 -0.240 0.927 4.000
END
------------------------------------------------------
--------command------------------
tleap -s -f leaprc.ff99SB
f = loadpdb "wat2.pdb"
saveamberparm f org.top org.crd
quit
--------------------------------
"Modified" version is by my manual change to ignore the nonbonded
interactions between 2 waters. I only changed topology file, not
coordinate file. Please see the 2 files below.
----------"original topology file(part)"-org.top---------------
%VERSION VERSION_STAMP = V0001.000 DATE = 11/09/10 16:54:06
%FLAG TITLE
%FORMAT(20a4)
%FLAG POINTERS
%FORMAT(10I8)
6 2 6 0 0 0 0 0 0 0
8 2 0 0 0 2 0 0 2 1
-
-
-
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
2 1 1 2 1 1
%FLAG NONBONDED_PARM_INDEX
-
-
-
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 3 0 5 6 6 0
%FLAG HBOND_ACOEF
--------------------------------------------------
----------"modified topology file(part)"-mod.top ---------------
%VERSION VERSION_STAMP = V0001.000 DATE = 11/09/10 16:54:06
%FLAG TITLE
%FORMAT(20a4)
%FLAG POINTERS
%FORMAT(10I8)
6 2 6 0 0 0 0 0 0 0
16(here) 2 0 0 0 2 0 0 2 1
-
-
-
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
5 4 3 2 1 1
%FLAG NONBONDED_PARM_INDEX
-
-
-
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 3 4 5 6 4
5 6 5 6 6 0
%FLAG HBOND_ACOEF
--------------------------------------------------
>i'm not sure why you say sander does not work
This means that...
sander -O -i min.in -o min_org.out -p org.top -c org.crd
sander -O -i min.in -o min_mod.out -p mod.top -c org.crd
and I run diff command between min_org.out and min_mod.out,
but they are the same except for time information e.t.c..
Although When I run diff command between anal_org.out and
anal_mod.out below, Anal says that nonbonded interaction
energies of modified topology file is not the same as the
original, there is no interaction between wat1 and wat2 in
the modified.
anal -O -i anal.in -o anal_org.out -p org.top -c org.crd
anal -O -i anal.in -o anal_mod.out -p mod.top -c org.crd
Best Regards,
Akihiro Yokota
-----Original Message-----
From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
Sent: Tuesday, November 09, 2010 9:04 PM
To: AMBER Mailing List
Subject: Re: [AMBER] "excluded atoms" declaration
i'm not sure why you say sander does not work- please explain what you did
and what the result is. you only specified for anal.
what are the "original" and "modified" versions?
2010/11/9 <Yokota_Akihiro.takeda.co.jp>
> ----------------------------
> Sorry to send a mail again.
> The title in my previous mail was blank.
> ----------------------------
>
> Dear AMBER Users,
>
> I am studying the topology file of AMBER to modify it,
> especially for "excluded atoms" declaration. And I found
> a mysterious things below. Do you have any suggestions or
> comments to me?
>
> Let me explain you in a simple case.
>
> 1. An original pdb file have only 2 water molecules, separated in 4A.
> 2. I changed the topology file, to ignore the nonbonded interactions
> between 2 water molecules.
> -> 3 points are modified(NEXT number in 8th line,
> %FLAG_NUMBER_EXCLUDEDATOMS,
> and %FLAG_EXCLUDED_ATOMS_LIST)
> 3. I checked the interaction energies of modified one by using Anal module.
> Anal said that nonbonded interaction between 2 waters is zero. This is
> OK.
> 4. And optimization by Sander module is performed, but the results from the
> original and the modified are definitely the same. Why does my
> "excluded atoms" declaration not work in Sander?
> (This indicate that Anal module correctly recognizes the "excluded atoms"
> declaration in topology file, and the sander module does not.)
>
> Do you have any suggestions or comments to me?
>
> Thanks in advance,
> Akihiro Yokota
>
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Received on Tue Nov 09 2010 - 17:00:02 PST
