From: PRITI ROY (priitii.roy_at_gmail.com)
Date: Tue Mar 21 2017 - 08:25:08 CDT
Dear NAMD experts,
I am trying to minimize (NAMD version 2.12) one dimeric protein of 354
residues using C-22 force field with periodic boundary condition. The first
and last residue is SER and ALA respectively and has four (4) disulfide
bond in one monomer and as same as another monomer. I have been generate
psf file using pasfgen package by adding NTER, CTER, DISU (for all
disulfide bond) patch and solvating the protein in water box. After that,
during minimization, I find the following error and adding corresponding
psf file of such error:
1.*FATAL ERROR: Atom 1 has bad hydrogen group size. Check for duplicate
bonds*
* (Monomer 1)*
*!NBOND: bonds*
* 1 5 2 1 2 1
3 1 3 1 4 1 4 1
5 6 *
*2.**FATAL ERROR: Atom 2776 has bad hydrogen group size. Check for
duplicate bonds** (Monomer 2)*
*!NBOND: bonds*
* 2776 2780 2777 2776 2777 2776 2778 2776
2778 2776 2779 2776 2779 2776 2780 2781*
*3.**FATAL ERROR: Duplicate bond from atom 2773 to atom 2775*
* (Monomer 1)*
*!NBOND: bonds 2769 2770 2769 2771 2769 2772
2773 2775 2773 2774 2773 2775 2773 2774 2773
2767**4. **FATAL ERROR: Duplicate bond from atom 5548 to atom 5550*
* (Monomer 2)!NBOND: bonds*
* 5544 5545 5544 5546 5544 5547 5548 5550
5548 5549 5548 5550 5548 5549 5548 5542*
The error no. 1 & 2 are in N-ter and 3 & 4 are in C-ter of the respective
monomer. So, my concern is the underlying reasons of generating multiple
bonds of these particular residues not anyother. I have seen the posts on
this topic but I could not sorted out the reason.
Hope you guys help me to understand and solving this problem.
Thanking you,
Priti Roy
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