From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Mon Mar 13 2017 - 11:56:01 CDT

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
>
>
>
>
>
> **
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-- 
*******************************************
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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