Re: [AMBER] ff10 from amber11 maybe not using OL3??

From: Amparo Garcia Lopez <Amparo.GarciaLopez.unige.ch>
Date: Thu, 16 May 2013 21:44:00 +0000

One last question, Pavel. I'm probably being a bit thick here, but what exactly do you mean by "adenine and guanine should have different atom types of their C8 carbons and similarly pyrimidines have different atom types of C5 and C6 carbons"?

I've looked at the pdb and prmtop files after parametrization, but C8 is C8 with or w/o chiOL3. I've also looked at the all_nucleic10.lib but can't compare with nucleic10.lib as I don't have it. Where do I look for what exactly?

Thanks very much again for your amazingly quick and helpful replies,
Amparo

Amparo Garcia-Lopez, Ph.D.

Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland

Tel: +41 (0)22 379 3376
Fax: +41 (0)22 379 3360

e-mail: Amparo.GarciaLopez.unige.ch
________________________________________
From: Amparo Garcia Lopez [Amparo.GarciaLopez.unige.ch]
Sent: 16 May 2013 23:16
To: AMBER Mailing List
Subject: Re: [AMBER] ff10 from amber11 maybe not using OL3??

Thanks both for your reply. So after doing all the tests you suggested I can confirm I've been unawareringly using an amber ff10 without the chiOL3 correction. Also, I can confirm that the person who installed amber11 in our machines used AmberTools 1.4.

I'll just have to redo all the work, I guess I've learnt my lesson well...

Thanks very much again for your help!

Amparo Garcia-Lopez, Ph.D.

Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland

Tel: +41 (0)22 379 3376
Fax: +41 (0)22 379 3360

e-mail: Amparo.GarciaLopez.unige.ch
________________________________________
From: pavel.banas.upol.cz [pavel.banas.upol.cz]
Sent: 16 May 2013 22:16
To: AMBER Mailing List
Subject: Re: [AMBER] ff10 from amber11 maybe not using OL3??

Dear all,
to my best knowledge, this is connected with version of Ambertools rather
than with Amber version. As I remember, there was a version of Ambertools
1.4 that had ff10 without chiOL3 correction, just ff99SB+bsc0 (I assume it
was revised very soon as most of amber11 compilations on our clusters
involve chiOL3). You can easily check it as the old version (without chiOL3
in ff10) has library for nucleic acids called "all_nucleic10.lib" (located
in its $AMBERHOME/dat/leap/lib directory), while the new version with chiOL3
uses nucleic10.lib.

Anyway, adenine and guanine should have different atom types of their C8
carbons and similarly pyrimidines have different atom types of C5 and C6
carbons.

have a nice day, Pavel

--
Pavel Banáš
pavel.banas.upol.cz
Department of Physical Chemistry,
Palacky University Olomouc
Czech Republic
---------- Původní zpráva ----------
Od: Niel Henriksen <niel.henriksen.utah.edu>
Datum: 16. 5. 2013
Předmět: Re: [AMBER] ff10 from amber11 maybe not using OL3??
"Use the rdparm program or some other prmtop reading program and check.
For instance, I just looked at one of my prmtop files:
---------------------------------------------------------------
> rdparm aaaa/vac.topo
\-/
-/- Welcome to RDPARM (an interactive utility for reading AMBER topology
files)
/-\ Type "help" or "?" for more information
\-/
-/- Version: "AMBER 12.0 integrated" (4/2012)
/-\
Residue labels:
A5 A A A3
RDPARM MENU. Please enter commands. Use "?" or "help"
for more info. "exit" or "quit" to leave program...
RDPARM MENU: dihedrals :1.O4'
.... blah
.... blah
253: 0.966 1.20 1.0 :1.O4' :1.C1' :1.N9 :1.C8 (8,9,11,12)
E 254: 1.074 0.27 2.0 :1.O4' :1.C1' :1.N9 :1.C8 (8,9,11,12)
E 255: 0.458 2.99 3.0 :1.O4' :1.C1' :1.N9 :1.C8 (8,9,11,12)
E 256: 0.309 0.33 4.0 :1.O4' :1.C1' :1.N9 :1.C8 (8,9,11,12)
.... blah
.... blah
> cat $AMBERHOME/dat/leap/parm/parm10.dat
.... blah
OS-CT-N*-C5 1 0.96561 68.7902 -1. ol3 chi ade
OS-CT-N*-C5 1 1.07403 15.6360 -2. ol3 chi ade
OS-CT-N*-C5 1 0.45754 171.5787 -3. ol3 chi ade
OS-CT-N*-C5 1 0.30917 19.0921 4. ol3 chi ade
.... blah
----------------------------------------------------------------------------
--------------
So you can see that I have the ol3 parameters in my prmtop (rdparm lists in
radians instead of degrees).
Best,
--Niel
________________________________________
From: Amparo Garcia Lopez [Amparo.GarciaLopez.unige.ch]
Sent: Thursday, May 16, 2013 10:31 AM
To: AMBER Mailing List
Subject: [AMBER] ff10 from amber11 maybe not using OL3??
Dear amber users,
there's this mistery I'd really appreacite if you could help me solve. I've
attached some snapshots, in case they help visualize what I'm saying.
I have been running explicit solvent MD (400 ns) of different RNA hairpin
molecules using amber11 and the ff10 for parametrization. For each molecule
I've done several replicates.
After some time during the trajectories, some of the replicates start
looking somehow unhappy and form an elongated, ladder-like structure rather
than the expected hairpin.
(something looking somehow like this http://ars.els-cdn.com/content/image/1-
s2.0-S0006349505732355-gr4.jpg but keeping the base pairings)
I also noticed that the OH group in the backbone sugars were very rigid
during the trajectories. As I understand, both this OH rigidity and this
tendency to form a ladder were force field problems in the past, which were
solved in the ff10 of amber after including the barcelona and OL3
modifications.
Now, I went to check my xleap log files to make sure that I had used the
right parameters. I was a bit surprised to see that when xleap loaded the ff
10 it said: PARM99 + frcmod.99SB + frcmod_parmbsc0 (see attachment for a
snapshot), without mentioning the OL3. I didn't know whether this meant that
the OL3 hadn't been loaded, or whether xleap simply doesn't tell you that it
loads it. So, I asked a friend who works in a different lab, to check what
happened when he parametrized my molecules with the ff10 using his amber11
installation. In his leap.log file he did have the chiOL3 bit!! (see
snapshot). In addition, he continued and run my molecule for 250ns, and at
least until that point the OH in the sugars were moving happily. I'm not
talking about subjective impressions here, I've been actually measuring
distances and angles to compare the two simulations.
The next thing I checked was this: Although I've been using amber11, in my
lab we have both amber11 and amber12. ff10 should be in both versions of
amber, so I compared the parm.10 and leaprc.ff10 files from my amber11 and
amber12 folders. To start with, the size of the files was different
depending on my version of amber. Maybe this means nothing. But, also, at
the top of the parm10.dat files, you can see this:
amber11: PARM99 + frcmod.99SB + frcmod_parmbsc0
amber12: PARM99 + frcmod.99SB + frcmod_parmbsc0 + OL3 for RNA
you see this difference also in the leaprc.ff10 file, and when you load the
force field in xleap (see snapshots).
I don't want to start panicking and want to believe that maybe with my amber
11 I'm still including the OL3 even though my files do not explicitly
mention it. But I'm actually a bit worried, especially after seing my
results vs my friend's. Could anyone using amber11 please tell me what they
see in their parm10.dat and leap.log files? Could someone please tell me how
I can be 100% sure whether or not I'm including the OL3 parm modification?
I really appreciate your suggestions. And if they mean bad news then I'd
also like to find out asp so I can start redoing the work.
Thanks again!
Amparo Garcia-Lopez, Ph.D.
Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland
Tel: +41 (0)22 379 3376
Fax: +41 (0)22 379 3360
e-mail: Amparo.GarciaLopez.unige.ch
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Received on Thu May 16 2013 - 15:00:02 PDT
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