Re: Martini CG models parameters errors

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Sep 26 2016 - 10:48:56 CDT

Hi Mahad,

I don't recognize the P5C atomtype, as its not standard CHARMM. I'm
guessing its a martini atomtype, which means that there should be a P5C
term in the nonbonded section of the parameter file you have still
loaded. If there isn't one, that is your problem. :) If you look at the
psf/pdb pair in VMD, what atoms have the P5C type? It could be that it
represents a non-protein component, which probably wouldn't be the the
amino acids file.

-Josh

On 09/26/2016 03:01 AM, Mahad Gatti wrote:
> Hi Josh,
>
> many thanks for the answer. I did like you said and I kept only the:
>
> parameters toppar/martini_v2.2_aminoacids.auto.namd.cons.prm
>
> while commenting the line:
>
> #parameters ../toppar_water_ions_namd.str
>
> but now I get this error:
>
> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE P5C
>
> Am I (again) loading the wrong parameters?
>
> Best regards,
>
> Mahad
> ________________________________________
> Da: Vermaas, Joshua [Joshua.Vermaas_at_nrel.gov]
> Inviato: giovedý 22 settembre 2016 17.36
> A: namd-l_at_ks.uiuc.edu; Mahad Gatti
> Oggetto: Re: namd-l: Martini CG models parameters errors
>
> Below is the offending line. OC is an atomtype in toppar_water_ions, but
> only as an NBFIX term. The file doesn't provide VDW information for that
> atomtype though (normally I think the protein or lipid file handles
> that), and so you get the error. If you are using martini, why would you
> need TIP3 water parameters anyway? Just comment out the line, as I
> suspect the martini parameter file will give you the parameters you need
> for the coarse grained water I hope you are using.
>
> -Josh
>
> On 09/22/2016 09:14 AM, Mahad Gatti wrote:
>> parameters ../toppar_water_ions_namd.str
>
>

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