VMD-L Mailing List

From: Nick Palmer (tuf90798_at_temple.edu)
Date: Wed Jun 20 2018 - 13:28:08 CDT

Hello everyone,

I am attempting to create a topology file for a new residue, it mostly
seems to be working however when used with autoPSF, the new residue is
treated as a separate chain and does not connect with the whole protein
chain. Here is what may be relevent to the problem in my topology file:

I have two new residues, one for the completely new residue, and one for a
slightly modified phenylalanine that is directly before the residue.

for the new residue:
BOND C CA3 CA3 N3 N3 C2 C2 CA2 CA2 N2
BOND HB1 CB2 CB2 CG2 CG2 CD1 CD1 HD1
BOND HE1 CE1 CE1 CZ CZ OH OH HZ
BOND HE2 CE2 CE2 CD2 CD2 HD2
BOND CA3 HA1 CA3 HA2
BOND N3 C1 C1 CA1 CA1 CA CA CG1 CG1 SD SD CE
BOND CA HB11 CA HB12 CG1 HG11 CG1 HG12 CE HE11 CE HE12 CE HE13
BOND N1 -CP
DOUBLE C O3 N2 C1 CB2 CA2 CD2 CG2 CE1 CD1 CZ CE2 CA1 N1

For the slightly modified PHE:
BOND CP CAP CAP N N HN
BOND CAP CBP CBP CGP CGP CD1P CD1P HD1P
BOND HE1P CE1P CE1P CZP CZP HZP
BOND HE2P CE2P CE2P CD2P CD2P HD2P
BOND CBP HB1P CBP HB2P
BOND N -C
DOUBLE CP OP CD2P CGP CD1P CE1P CE2P CZP

The new residue and the PHE are connected however both of them are seperate
from the rest of the chain. I have been playing around with it for a while
and trying to find an answer somewhere online but so far I haven't found
anything.

Thank you for your help in advance! 

-- 
Nicholas J. Palmer