Re: [AMBER] tleap hangs when tries to read new residue

From: Bill Ross <>
Date: Mon, 07 Oct 2019 02:52:14 -0700

If you see cpu at 100% while results remain 0%, I will make a convert of you yet. I don't remember the debug stuff. Did you look at leap.log? Debugging is about isolating, e.g. your res in it's own file. Or go to the source, and say Darth sent you. :-)AI:
-------- Original message --------From: Dawid das <> Date: 10/7/19 2:40 AM (GMT-08:00) To: AMBER Mailing List <> Subject: Re: [AMBER] tleap hangs when tries to read new residue Dear Bill,Thank you for your answer. I have checked my topology and it looks fine.Is it possibly to make tleap produce more output data (make it moreverbose/noisy)?Perhaps it would let me to find the source of this issue.Best wishes,Dawid Grabarekniedz., 6 paź 2019 o 21:49 Bill Ross <> napisał(a):> Better to put your own res in its own file too.>> Bill>> On 10/6/19 12:48 PM, Bill Ross wrote:> >> > Sounds like you may have a topological problem in your residue> > definition that causes an infinite loop.> >> > Bill> >> > On 10/6/19 10:09 AM, Dawid das wrote:> >> Dear Amber Users,> >>> >> I have a protein which contains a modified amino acid (SYN) that is> >> covalently bonded to both proceeding and following natural amino acids.> >>> >> Now, I have the parameters ready for SYN so I put them into> >> the parm99.dat file. Also, I have defined the SYN in my library> >> file (all_amino94ildn.lib) together with all the other amino acids.> >>> >> When I run> >> tleap -f > tleap.out> >>> >> it hangs while loading the amino acids library:> >> Loading library:> >> /home/dawid/Programy/AmberTools/amber18/dat/leap/lib/all_amino94ildn.lib> >> Loading: ALA> >> Loading: ARG> >> Loading: ASH> >> Loading: ASN> >> Loading: ASP> >> Loading: CYM> >> Loading: CYS> >> Loading: CYX> >> Loading: GLH> >> Loading: GLN> >> Loading: GLU> >> Loading: GLY> >> Loading: HID> >> Loading: HIE> >> Loading: HIP> >> Loading: ILE> >> Loading: LEU> >> Loading: LYN> >> Loading: LYS> >> Loading: MET> >> Loading: PHE> >> Loading: PRO> >> Loading: SER> >> Loading: SYN> >>> >> It always happens at this stage. I have tried to create a separate> >> library for SYN residue and use loadOff but then I get an error message> >> saying that atom types for SYN are unknown even though I have defined> them.> >>> >> What could be the source of this issue?> >> I attach my file.> >>> >> Best wishes,> >> Dawid Grabarek> >>> >> _______________________________________________> >> AMBER mailing list> >>> >>> _______________________________________________> AMBER mailing list>>>_______________________________________________AMBER mailing listAMBER.ambermd.org
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Received on Mon Oct 07 2019 - 03:00:02 PDT
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