RE: Martini CG models parameters errors

From: Mahad Gatti (Mahad.Gatti_at_iit.it)
Date: Mon Sep 26 2016 - 04:01:32 CDT

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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