You have to look at the .lib or .mol2 files in order to see the atom
types. For adenosine and guanosine, chi torsion requires the definitions
of parameters for O4'-C1'-N9-C8, C2'-C1'-N9-C8, O4'-C1'-N9-C4, and
C2'-C1'-N9-C4. For cytidine and uridine, parameters will define
O4'-C1'-N1-C2, C2'-C1'-N1-C2, O4'-C1'-N1-C6, and C2'-C1'-N9-C6 torsions.
Depending on which version of chi revision you use, the parameters will
vary. In amber99CHI_YIL, we defined the atom type of C8 to be C1 and C2
for adenosine, and guanosine, respectively. The same notation was followed
by the group who created the chiOL parameters. Check out the following
.lib file in order to get a better understanding of the atom types:
$AMBERHOME/dar/leap/lib/residues.RNA.parmCHI_YIL.bsc.lib
Look at the atom types of atom name C8 in adenosine and guanosine, and C6
in cytidine and uridine.
Best regards,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Thu, 16 May 2013, Amparo Garcia Lopez wrote:
> 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 - 15:30:02 PDT
