Tutorial-l Mailing List

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Mon Mar 13 2017 - 13:22:46 CDT

Hi,

NAMD can read multiple files with no problem. However, if you
downloaded the original CHARMM files, you may have to edit them a bit to
comment out the lines containing CHARMM code (if loops, "read card"
lines etc) which NAMD does not recognize.

You can find NAMD-formatted CHARMM36 files in your VMD installation, in
the readcharmmtop and readcharmmpar plugin directories. Try using those.

Fotis

On 03/13/2017 08:10 PM, esserlo_at_helix.nih.gov wrote:
> Hi, Fotis,
>
> thanks this makes sense. I used vmd 1.9.3 throughout. I think it would make
> sense to use the newer parameter files. After I downloaded
> toppar_c36_jul16.tgz, I could potentially use par_all36_prot.prm and
> par_all36_lipid.prm -- but do I have to combine the parameter files into one
> file (would cat *.prm > all.prm work) or can NAMD read multiple prm files ?
>
> Thanks,
>
> Lothar
>
>
>> Hello Lothar,
>>
>> From what I see, you've built your membrane using a CHARMM36 (C36)
>> topology (that's where the OSLP atom appears for POPC, C27 POPC still
>> has them named as OSL) and you're trying to simulate your system using
>> CHARMM27 (C27) parameters. It's only natural that your simulation fails.
>>
>> Try building your system again using the same force field for all
>> components (either C36 or C27) and use the appropriate FF parameters for
>> your simulation.
>>
>> A note of caution: since version 1.9.3, VMD has moved on from C27 and
>> now uses C36 as its "default" force field in many of its
>> extensions/applications (e.g. for the psf builder, for QwikMD and
>> others). As such, if you want to use the C27 force field you have to
>> define it (for example, include a "topology
>> (place_of_ff)/top_all27_prot_lipid_na.inp" line in your psfgen scripts).
>>
>> HtH,
>>
>> Fotis
>>
>> On 03/13/2017 05:16 PM, esserlo_at_helix.nih.gov wrote:
>>> Hi,
>>>
>>> I am using Paween Mahinthichaichan's Membrane Proteins Tutorial 2016 and
>>> tutorial files but I am hitting a snag at the very first run of NAMD.
>>>
>>>
>>> $namd2 kcsa_popcwimineq-01.conf
>>>
>>> stops with:
>>>
>>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OSLP
>>>
>>> The ../par_all27_prot_lipidNBFIX.prm does not contain atom type OSLP just
>>> OSL
>>>
>>> Is there an updated version of par_all27_prot_lipidNBFIX.prm ? Or am I
>>> missing
>>> something else ?
>>> Note I used the vmd membrane protein plugin to generate the membrane and its
>>> psf file does contain atoms of type OSLP: Line 157 in popc.psf: POPC O12
>>> OSLP
>>> ....
>>>
>>> Thanks,
>>>
>>> Lothar
>>>
>>>
>>>
>>>
>>>
>>> **
>>> ** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
>>> **
>> --
>> *******************************************
>> Fotis A. Baltoumas
>> Phd Candidate, Bioinformatics Postgraduate Programme
>> Department of Cell Biology and Biophysics
>> Faculty of Biology, University of Athens
>> Panepistimiopolis, Athens 157 01, GREECE
>> --------------------------------------
>>
>> email : fbaltoumas_at_biol.uoa.gr
>> http://biophysics.biol.uoa.gr
>> http://bioinformatics.biol.uoa.gr
>> *******************************************
>>
> 

-- 
*******************************************
Fotis A. Baltoumas
Phd Candidate, Bioinformatics Postgraduate Programme
Department of Cell Biology and Biophysics
Faculty of Biology, University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
*******************************************
**
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