[gmx-users] Re: about beta port of C27 FF to gromacs

Pär Bjelkmar bjelkmar at cbr.su.se
Mon Jan 25 10:34:42 CET 2010

Hi Alexandar,

I redirected my answer to the gmx-users mailing list so it's available to all users. 

23 jan 2010 kl. 22.41 skrev Alexandar T Tzanov:

> Hi  Par,
> I downloaded your 'Charmm to Gromacs port v1.1" and tried it on my simple 
> system - NATMA (ACE-TRP-NAC total 36 atoms).  I used 
> pdb2gmx -f natma.pdb -ff charmm27 -o natma1.pdb  -ter -water tip3p
> and got: 
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 3 residues with 36 atoms
>  chain  #res #atoms
>  1 'X'     3     36  
> All occupancies are one
> Opening library file /usr/local/gromacs/share/gromacs/top/ffcharmm27.atp
> Atomtype 1
> Reading residue database... (ffcharmm27)
> Opening library file /usr/local/gromacs/share/gromacs/top/ffcharmm27.rtp
> Residue 1
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.7
> Source code file: resall.c, line: 344
> Fatal error:
> in .rtp file in residue cmap at line:
> 	-C	N	CA	C	+N
> :q!
> -------------------------------------------------------
> I am wondering if there is a bug in a code or I am doing something wrong.
> My gromacs is latest available - 4.0.7 

Well, the CHARMM source is not available in version 4.0.7 but in git head (it will be part of version 4.1) so you have to pull the latest git source. 

Having said that, there might very well be something wrong when using ACE termini since it has to be treated a bit specially in GROMACS (i.e. as a residue rather than in the termini db, as is also the case in the amber port) and this particular termini has not been tested by us. I don't know what residue/termini NAC is but nothing with that name is present in the CHARMM top file I'm parsing. 

To use a ACE termini, you need to have the coordinates of the ACE also in the input file (since it's a residue by itself and will not be generated by pdb2gmx) and it has to have it's own residue number. Then you select the None N-"termini". (Correct me somebody if I'm wrong). You could send me your input coordinate file if this doesn't help and I'll take a look at it.

Pär Bjelkmar

> Thanks 
> Alex
> ===================
> Alexander Tzanov
> New York University
> Department of Chemistry
> 100 Washington Square East, Room 1001U
> New York, NY 10003
> Phone: 212-998-3589
> Fax: 212-995-4475
> Email: alex.tzanov at nyu.edu

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