VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Jun 20 2018 - 21:10:23 CDT

Hi Nick,
The best way to deal with this in autopsf is to manually select the chains
-- you can do this in the command line or GUI (the command line using the
-include option, or the gui in the "Chains identified" box). If you set up
your protein chain to include the modified residues, it should work fine.
Best,
Peter

On Wed, Jun 20, 2018 at 12:28 PM, Nick Palmer <tuf90798_at_temple.edu> wrote:

> 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
>