Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1

From: ramya narasimhan (ramya_jln_at_yahoo.co.in)
Date: Tue Nov 11 2008 - 22:18:25 CST

Thanks for your quote. But still I can't change it to HC in pdb and psf file as there are 3 hydrogen atoms. It is not possible to change all the 3 as HC. How to solve it?
Thanks in advance.
Ramya.L.

--- On Tue, 11/11/08, Giacomo Fiorin <gfiorin_at_seas.upenn.edu> wrote:
From: Giacomo Fiorin <gfiorin_at_seas.upenn.edu>
Subject: Re: namd-l: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1
To: ramya_jln_at_yahoo.co.in
Cc: "namdmail" <namd-l_at_ks.uiuc.edu>
Date: Tuesday, 11 November, 2008, 8:28 PM

You are right, in the parameter file "HT1" is missing, because it
identifies an atom, not a type. The PSF file you are using is not
entirely with the CHARMM parameter file: the atom whose name is "HT1"
should have a type "HC" instead.

Giacomo

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On Tue, Nov 11, 2008 at 4:23 AM, ramya narasimhan <ramya_jln_at_yahoo.co.in>
wrote:
> Hi All,
> I minimized and equilibrated the protein using CHARMM22 ff.
When
> I tried for production run, it is giving the following error.
>
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1
>
> Actually this HT1, HT2 and HT3 are for the NTER residue. In the parameter
> file, HT is present and is for TIP3P water molecule. How to get rid of
this
> problem?
>
> Thanks in advance.
> Ramya.L.
>
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