VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Dec 28 2010 - 19:01:22 CST

Dong Luo posted an answer on 12/22 that is exactly what I was going to
suggest; I'm pretty sure the problem here is that the input pdb had a
CT2 residue instead of properly attempting to use a CT2 patch.
Best,
Peter

On 12/28/2010 06:03 PM, Jim Phillips wrote:
>
> Is there any useful psfgen output preceeding that final error?
>
> -Jim
>
>
> On Wed, 22 Dec 2010, Francesco Pietra wrote:
>
>> To be more specific, autopsf recognizes the CT2 segment as
>> non-protein. Therefore, in the gui I edit:
>>
>> -- the PHE segment 1-81, adding 82-86 in a single segment 1-86
>>
>> --N terminal patch, from NTEr to CT2
>>
>> --C terminal patch from CTER to CT2
>>
>> -- delete the 82-86 segment
>>
>> --Selection from 'everything' to 'protein'
>>
>> The display now shows the entire PHE-CT2
>>
>> I have tried other combinations in the gui but always ending in "
>> error: failed on end of segment". Either (very likely) my procedure is
>> incorrect or autopsf gets confused by CT2. I have considered related
>> problems on the VMD mail list.
>>
>> thanks
>>
>> francesco
>>
>>
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret_at_gmail.com>
>> Date: Tue, Dec 21, 2010 at 6:49 PM
>> Subject: vmd-l: autopsf error: failed on end of segment
>> To: vmd-l_at_ks.uiuc.edu
>>
>>
>> Hello:
>> With VMR 1.8.7 I am trying to generate psf for a protein ending with
>> amidated phenylalanine, using validated top_all27_prot_na.rtf. I tried
>> also 'source autopsf.tcl', using a recent script, before autopsf. It
>> always crashes with error: failed on end segment.
>>
>> The pdf file ends with (here I tried separately chain D, renumbering
>> atoms) using the method for amber:
>>
>> ATOM 80 HE2 PHE D 4 -31.197 22.536 3.559 1.00 0.00
>> 4SG H
>> ATOM 81 HZ PHE D 4 -30.544 24.713 4.555 1.00 0.00
>> 4SG H
>> ATOM 82 C CT2 D 5 -32.820 18.877 8.926 1.00 0.00
>> 4SG C
>> ATOM 83 O CT2 D 5 -34.065 18.451 9.222 1.00 0.00
>> 4SG O
>> ATOM 84 NT CT2 D 5 -31.788 18.180 9.397 1.00 0.00
>> 4SG N
>> ATOM 85 HT2 CT2 D 5 -30.844 18.477 9.196 1.00 0.00
>> 4SG H
>> ATOM 86 HT1 CT2 D 5 -31.949 17.354 9.956 1.00 0.00
>> 4SG H
>>
>> Is that correct?
>>
>> Thanks for help
>>
>> francesco pietra
>>