From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Dec 10 2019 - 18:09:24 CST
How was the psf generated? NAMD is complaining that it can't find a parameter for an atomtype listed in the psf, in this case N287. This isn't a standard CHARMM atomtype, so I suspect you'll need to regenerate your psf correctly.
-Josh
On 2019-12-10 11:20:54-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
Adupa,
Yes the attached molecule is there too, can you please tell me how to make the parameter for it?
Thanks a lot
On Tue, Dec 10, 2019 at 11:28 AM Adupa Vasista <adupavasista_at_gmail.com<mailto:adupavasista_at_gmail.com>> wrote:
Are there any other molecules other than protein? If so, then you have to add the parameters for that molecule too.
and while using CHARMM36, better add carb.prm separately instead of lipid_prot_carb.prm
On Tue, Dec 10, 2019 at 10:36 PM mohammad goodarzi <mo.goodarzi82_at_gmail.com<mailto:mo.goodarzi82_at_gmail.com>> wrote:
Hello,
I have read a number of posts but none answered me this question.
I am getting error as
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N287
Charm++ fatal error:
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N287
Abort trap: 6
and my parameters are
# Force-Field Parameters
paraTypeCharmm on
parameters ./par_all36_lipid_prot_carb.prm
parameters ./par_all36_lipid.prm
parameters ./par_all36_prot.prm
parameters ./par_all36_na.prm
I just don't know what to add more, whatever I add or remove I get the same error
Thanks
Mo
-- A.Vasista M.Tech,Department Of Chemical Engineering, IIT Guwahati.
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