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-- 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber" _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu May 16 2013 - 15:00:02 PDT