From: siddharth kamal (411cy5084_at_nitrkl.ac.in)
Date: Thu Jul 16 2015 - 07:44:46 CDT
Sir i have to generate psf file of heparin and heparan sulfate both with 6-monomers. Sir, in top_all36_carb.rtf there is no patch for nitrogen-sulfur linkage. So i searched for the patch between 'N' and 'SO3-' and i downloaded it from " http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=32450&page=1 ".
After the generation of psf file for heparin and heparan sulfate using psfgen (no error showing while generating the psf file), for the sulfate group one of the bond between S and O is very large compared to the other two S and O bonds and also all three bonds have different bond lengths. When i run the simulation to check Whether the structure i get the following error.
Reason: FATAL ERROR: Atom 26 has bad hydrogen group size. Check for duplicate bonds.
Fatal error on PE 0> FATAL ERROR: Atom 26 has bad hydrogen group size. Check for duplicate bonds.
All the file i am using for simulation are in attachment.
Here is the information, so i request you to help me out with this problem.
here is link for all the files i have used " https://www.dropbox.com/s/dfz3ety0jbytu3p/Fwd%20Regarding%20problem%20in%20generating%20psf%20file%20of%20heparin%20and%20heparan%20sulfate.zip?dl=0 "
for any other information plz reply me.
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