Dear Brendan,
I am working on this now.
In the meantime, I would suggest you to make and remove the
bonds in some GUI program and save the result in mol2 format.
Then load it in sleap and save prmtop, which would be much
easier.
Sincerely,
Wei
Brendan Duggan wrote:
> I tried to post this a few weeks ago but it seems it never made it to
> the mailing list. My apologies if this is a repeat.
>
> I've been trying to create a prmtop file for a sphingolipid, however
> xleap (Amber9 and AmberTools versions) crashes and issues a
> "Segmentation fault" when I issue the SaveAmberParm command. The
> AmberTools version of xleap gives a bit more information on crashing.
> Here's the output I get:
>
>
>> /opt/amber10/bin/xleap -s -f glccer.leaprc
>>
> -I: Adding /opt/amber10/dat/leap/prep to search path.
> -I: Adding /opt/amber10/dat/leap/lib to search path.
> -I: Adding /opt/amber10/dat/leap/parm to search path.
> -I: Adding /opt/amber10/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source glccer.leaprc.
> /opt/amber10/bin/xleap: line 9: 13401 Segmentation
> Fault /opt/amber10/bin/xaLeap -I/opt/amber10/dat/leap/prep -
> I/opt/amber10/dat/leap/lib -I/opt/amber10/dat/leap/parm -
> I/opt/amber10/dat/leap/cmd $*
>
> The number between "line 9" and "Segmentation fault" changes with each
> crash. The file "glccer.leaprc" is as follows:
>
> source leaprc.gaff
>
> # load residues
> LoadAmberPrep stearate.prepin
> LoadAmberPrep sphingosine.prepin
> LoadAmberPrep glucose.prepin
>
> # set connection atoms to link residues
> set STE.1 connect1 STE.1.C1
> set STE tail STE.1.C1
> set SPH.1 connect0 SPH.1.N2
> set SPH.1 connect1 SPH.1.O1
> set SPH head SPH.1.N2
> set SPH tail SPH.1.O1
>
> # combine residues into one new molecule
> GLCCER = sequence { STE SPH GLC }
>
> # correct incorect Glucose linkage
> deletebond GLCCER.2.O1 GLCCER.3.O4
> bond GLCCER.2.O1 GLCCER.3.C1
>
> # remove atoms eliminated in linkages
> remove GLCCER GLCCER.STE.O1'
> remove GLCCER GLCCER.STE.HO1
> remove GLCCER GLCCER.SPH.HN23
> remove GLCCER GLCCER.SPH.HO1
> remove GLCCER GLCCER.GLC.H11
>
> # make double bond b/w SPH C8 and C9
> remove GLCCER GLCCER.SPH.H83
> remove GLCCER GLCCER.SPH.H93
>
> # make hydroxyl at STE C2
> set GLCCER.STE.H23 name O2
> set GLCCER.STE.O2 element O
> set GLCCER.STE.O2 type oh
> set GLCCER.STE.O2 charge -0.62703
> h1 = CreateAtom HO2 ho 0.417
> set h1 element H
> add GLCCER h1
> bond GLCCER.STE.O2 h1
>
> # save prmtop and inpcrd files
> SaveAmberParm GLCCER glccer.prmtop glccer.inpcrd
>
> The prep files stearate.prepin, sphingosine.prepin and glucose.prepin
> were prepared using GAFF and are attached.
>
> Can anyone tell me what I'm doing wrong?
>
> Brendan
>
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Received on Fri Apr 18 2008 - 21:19:37 PDT
