Re: using NAMD with CHARMM36 ff

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Jan 18 2015 - 12:32:35 CST

Seems like you probably didnít use charmm36 after all? Compare 36 and 27 and double check.

JC

On Jan 17, 2015, at 9:04 PM, Maria Bykhovskaia <mb.ucdelcaribe_at_gmail.com> wrote:

> JC,
> Thanks, that helped!
> However, now I am getting another error message:
>
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB
>
> It looks like the bilayer built with VMD denotes backbone H as "HB", and par_all36_lipid.prm file denotes this as "HBL"
> Should I change HB by HBL in my system?
> I wonder if it might be safer just continue using CHARMM27 rather than trying to address all the mismatches?
> Thanks,
> Maria
>
>
>
>
> On Sat, Jan 17, 2015 at 10:36 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> If I recall correctly, this comes from the NBFIX terms at the bottom of the water (?) parameter file. You could comment out those lines, just being careful to remember that you did so if you ever do have those atom types.
> JC
>
>
> On Jan 17, 2015, at 8:26 PM, Maria Bykhovskaia <mb.ucdelcaribe_at_gmail.com> wrote:
>
>> Hi,
>> I tried to use ChARMM36 force field, and I am getting the message:
>>
>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2
>>
>> my system does not have the atom type OC2D2
>>
>> It runs with Charmm27 without errors. The system includes a protein and membrane with water (TIP3) and ions (POT, CLA, CAL), psf was generated with VMD, and Charmm36 topology was used to build the lipid bilayer.
>>
>> My input file looks this way:
>>
>> paraTypeCharmm on
>>
>> parameters par_all36_lipid.prm
>>
>> parameters par_all36_prot.prm
>>
>> parameters par_all36_cgenff.prm
>>
>> parameters toppar_water_ions_namd.str
>>
>>
>> mergeCrossterms yes
>>
>> Will appreciate any suggestions.
>>
>> Thanks,
>>
>> Maria
>>
>>
>>
>>
>>
>>
>>
>
>
>
>
> --
> Maria Bykhovskaia
> Professor and Chair, Neuroscience Department
> Director, Specialized Neuroscience Research Program
> Universidad Central del Caribe
> Bayamon, Puerto Rico
> http://maria.ucdelcaribe.org
> http://neuro.ucdelcaribe.org
> http://SNRP.uccaribe.net
>

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