PSF of Tryptophane methyl ester

From: CHINDEA Vlad (
Date: Sat Oct 11 2008 - 11:43:43 CDT

Dear all

I am trying to prepare the PSF of this compound using AutoPSF, which should be easy since all elements are available in top_all27_prot (the aminoacid, NTER patch and CT1 methyl ester patch).

File was prepared in Molefacture in two different ways: either allready containing the methyl ester and N terminal hydrogen and either as bare TRP. Either way the result was the same. During AutoPSF everything looks Ok until in step 3 when pressing "Crate chains" , regardless if I removed with 'Edit chain' the automatic CTER and NTER, PSF File is generated indeed but with the methyl patch removed and following error is reported

error deleting "S-TME1_autopsf-temp.pdb": permission denied
error deleting "S-TME1_autopsf-temp.pdb": permission denied
    while executing
"file delete $tempfile "
    (procedure "clean_tempfiles" line 3)
    invoked from within
    (procedure "makepatches_gui" line 77)
    invoked from within
    (procedure "::autopsf::afterchains_gui" line 97)
    invoked from within
    invoked from within
".autopsf.chains.finish invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 24)
    invoked from within
"tk::ButtonUp .autopsf.chains.finish
    (command bound to event)

If in step 4 'Patches' if I try to add the CT1 patch it is added indded, but wrong bonding is established between the methyl and other parts of the molecule !

Any ideeas on what could be done ?

Many thanks
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