RE: charmm to namd conversion

From: Felipe Merino (
Date: Mon Jun 04 2012 - 16:39:55 CDT

Please keep the emails in the list. psfgen needs a segment to be defined mainly for each chain of your macromolecule (therefore it applies the correct patches to the terminal residues). Besides that often you create a segment for your ions and then some segments fr you water molecules dependig on how many of those you have. To do that you need a separate pdb for each segment.

Take a look here




----Mensaje original----De: Roarkma_at_wabash.eduFecha: 04-jun-2012 16:19Para: "Felipe Merino"<>Asunto: RE: namd-l: charmm to namd conversionI'm sorry, I meant to say ~1500 water molecules. ________________________________________From: Felipe Merino []Sent: Monday, June 04, 2012 2:37 PMTo: Matthew B. Roark; namd-l_at_ks.uiuc.eduSubject: Re: namd-l: charmm to namd conversionHi,What i do in those cases (just my personal opinion) is to create a pdb file with the coordinates and then create the psf from scratch in vmd. For me it is much cleaner. You just have to divide your pdb in several segments and to take care that none of those have more than the limit of residues per segment allowed by psfgen (i think it is 10k, but i am not sure) which is usually the case for the solvent. For the velocities (if you have them) you can just read then as coordinates and then ask vmd to write a binary file and the you can do you restart with fresh and appropriate files.bestFelipe----Mensaje original----De: Roarkma_at_wabash.eduFecha: 04-jun-2012 13:29Para: ""<>Asunto: namd-l: charmm to namd conversionI am having many problems getting a CHARMM simulation converted to NAMD-readable formats on a Rocks 5.1 cluster. My first method was to use CHARMM to write a psf in xplor formatand coordiantes in pdb format. NAMD complains:Fatal error on PE 0> FATAL ERROR: ABNORMAL EOF FOUND - buffer=*end*From what I could tell this is a formatting error in either the psf or pdb. Is it possible to distinguish which one is causing the problem?My next approach was to use scripts provided on the NAMD website (, charmm2namd and crd2pdb. Neither of these scripts work.Running charmm2namd results in:PSF EXT CMAP CHEQ 3 !NTITLE* RESIDUES WITHOUT PATCHING* DATE: 6/ 1/11 14: 0:58 CREATED BY USER: roarkma* Converted to NAMD format using ../toppar/toppar_all.str on Mon Jun 4 13:21:28 2012 79901 !NATOMTraceback (most recent call last): File "./charmm2namd", line 81, in ? linetuple=(int(line[0]),line[1],line[2],line[3],line[4],line[5],float(line[6]),float(line[7]),int(line[8]))ValueError: invalid literal for int(): 0 0.00000 -0.301140E-02I see that my psf has 11 columns and the script is reading the first 9, but somehow the script is using the last 3 columns combined. I'm not familiar with python so I am unsure how to fix this.Running crd2pdb results in:Traceback (most recent call last): File "./crd2pdb", line 27, in ? numofatoms = float(buffer)ValueError: invalid literal for float(): 79901 EXTThis is very frustrating. How much have these scripts been tested? I have tried 2 methods to use "compatible" formats and yet I have gotten zero progress. Can anyone shed some light on(1) doing the conversion within CHARMM or (2) troubleshooting the NAMD scripts?

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