VMD-L Mailing List

From: SONAL GAHLAWAT (sg1389_at_scarletmail.rutgers.edu)
Date: Thu Aug 10 2023 - 13:32:17 CDT

Hi,

I am trying to perform SMD on collagen-like peptides that I created using
the THeBuScr script using VMD and NAMD. I have already performed MD
Simulations on these peptides using Amber18.

For performing SMD, I generated .pdb and .psf files using the Automatic PSF
builder in VMD, then solvated the protein and neutralized the solvent. When
I run my first minimization of the prepared system, I get the following
error: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB2 CT1 NH3 (ATOMS
1 5 8).
I have attached my PDB and PSF files.

Any help in troubleshooting this will be greatly appreciated.
Thank you.

Regards,
Sonal Gahlawat

 GFPGER_Gly3_final.pdb
<https://urldefense.com/v3/__https://drive.google.com/file/d/1caNMBWCSi_Fvw3HYRUfdZ4TvrsLNhUc6/view?usp=drive_web__;!!DZ3fjg!5-XpGYkhTcaV-vIFxErsvtfPwlFAWJZXPWoFLiA9916RrE3_LU42Q7eCkzVxKLVzaVg73MV-8MhTKPwUCnu_cgjyroKt$ >
 GFPGER_Gly3_final.psf
<https://urldefense.com/v3/__https://drive.google.com/file/d/1aqQXM2KvjZ_LieEQzxh7RC5W7SNhSZGt/view?usp=drive_web__;!!DZ3fjg!5-XpGYkhTcaV-vIFxErsvtfPwlFAWJZXPWoFLiA9916RrE3_LU42Q7eCkzVxKLVzaVg73MV-8MhTKPwUCnu_cnikyOrh$ >