AMBER Archive (2009)

Subject: Re: [AMBER] Adding non standard residues

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Mon May 11 2009 - 16:11:49 CDT

Hi,

Thanks - I look at the generated pdb file from prmtop inpcrd using the
amdpdb so I presume it is okay.

Regarding changing the properties of the water molecule - i tried to change
the HW atom names from HW to PG but
MASS
PG 1.008

BOND
OW-PG 553.0 0.9572 TIP3P water
PG-PG 553.0 1.5136 TIP3P water

ANGLE
PG-OW-PG 100. 104.52 TIP3P water
PG-PG-OW 0. 127.74 (found in crystallographic water with 3
bonds)

NONBOND
PG 0.0000 0.0000 TIP3P water model

these parameters I have saved in the a mod.frcmod file which I load before
saving the parameters but ambertool gives me an error with unknown type PG
but it is available in both hoc.lib and as well in the frcmod file -

how to resolve this any hint appreciated

Thanks in advance

Best
J

On Mon, May 11, 2009 at 7:30 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Mon, May 11, 2009, Jorgen Simonsen wrote:
> >
> > I am trying to modify a water molecule and a cysteine residue from a
> crystal
> > structure - the two residues should be bonded to a nickel ion. I go
> through
> > tutorial 4 "*Simulating a Solvated Protein that Contains Non-Standard
> > Residues" *and create the cysteine residue from CYX to CYY and the water
> > from WAT to HOC residue names and save the two lib files
>
> > This gives me two problems - first of all the HW-HW is not recognized by
> > NAMD
>
> Can't help with the NAMD problem.
>
> > Marking per-residue atom chain types.
> > (Residues lacking connect0/connect1 -
> > these don't have chain types marked:
> >
> > res total affected
> >
> > CARG 1
> > CYY 1
> > HOC 1
> > NGLN 1
> > WAT 350
> > )
>
> I don't think this should cause problems, but you should check to be sure
> that
> the CYY residue is properly bonded to residues before and after it in the
> chain.
>
> ...good luck...dac
>
>
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