Re: PSF of Tryptophane methyl ester

From: Peter Freddolino (
Date: Sat Oct 11 2008 - 12:48:34 CDT

Hi Vlad,
did you build the tryptophan by hand or with the protein builder? Have
you verified that all of the atom naming matches that in the charmm
topology files? It will if you used the protein builder.

CHINDEA Vlad wrote:
> 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
What did you replace NTER/CTER with for those patches?
> error deleting "S-TME1_autopsf-temp.pdb": permission denied
> error deleting "S-TME1_autopsf-temp.pdb": permission denied
This is odd... what platform are you running on?
> 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 !
If my previous comments don't help, could you send me the pdb you end up


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