From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Dec 11 2019 - 12:28:56 CST
Rather than flaming the tutorials, you really ought to spend some time reading the documentation/instructions outside of the tutorials as well. You aren't providing the tool the inputs it needs, and its erroring as a result. CGenFF asks for a .pdb or a .mol file as an input. What you've copied is neither (a .gro file I think?), and so CGenFF can't parse the input file.
Slow down, explain what you are trying to do and provide enough detail so that others can understand what is going on. From reading between the lines, I think you've got a protein/benzene complex, and you'd like to run MD in water to do some free energy calculations, right? Step 1 would be to get this system running in equlibrium conditions, and then start worrying about the other pieces. Can you lay out how you built the system? Ideally with a script and a set of input files you could share to make the debugging process easier? The readership of this mailing list collectively has thousands of years of MD experience, but without a well formulated question, we really can't help.
On 2019-12-11 10:26:38-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
I used CGENFF for it. when I import the molecule parameters it gives error like error on the first line
LIGPARGEN GENERATED GRO FILE
1BNZ C00 1 -3.378 0.507 0.291
1BNZ C01 2 -3.455 0.482 0.404
1BNZ C02 3 -3.297 0.620 0.288
1BNZ H03 4 -3.381 0.439 0.207
1BNZ C04 5 -3.453 0.568 0.514
1BNZ H05 6 -3.518 0.395 0.406
1BNZ C06 7 -3.371 0.680 0.512
1BNZ H07 8 -3.515 0.548 0.601
1BNZ C08 9 -3.296 0.705 0.397
1BNZ H09 10 -3.366 0.747 0.596
1BNZ H0A 11 -3.234 0.793 0.394
1BNZ H0B 12 -3.235 0.641 0.202
1.00000 1.00000 1.00000
then I remove the first line and it give error on BNZ.
how should the parameter file look like?
On Wed, Dec 11, 2019 at 1:51 AM Adupa Vasista <adupavasista_at_gmail.com<mailto:adupavasista_at_gmail.com>> wrote:
Use CGENFF to get parameters.
On Tue, Dec 10, 2019 at 11:45 PM mohammad goodarzi <mo.goodarzi82_at_gmail.com<mailto:mo.goodarzi82_at_gmail.com>> wrote:
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:
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
I just don't know what to add more, whatever I add or remove I get the same error
-- A.Vasista M.Tech,Department Of Chemical Engineering, IIT Guwahati. -- A.Vasista M.Tech,Department Of Chemical Engineering, IIT Guwahati.
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