[gmx-users] CMAP error

[Thomas Piggot]

This is a completely separate issue where the CHARMM force field files 
from which the GROMACS CHARMM27 rtp entries were created do not have a 
DPPC entry, rather DPPC in CHARMM is created from using two residues 
(PALM and PCGL) and two patches (EST1 and EST2). It should have been 
easy enough to make a CHARMM27 DPPC rtp entry anyway.

Cheers

Tom

Amit Choubey wrote:
> This may not be related but it was not straight forward to do DPPC 
> membrane simulation using CHARMM FF in gromacs. The DPPC molecule was 
> not defined at all in the FF files.
> 
> The DPPC is defined in terms of two more residues in CHARMM.
> 
> amit
> 
> On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Jon Mujika wrote:
> 
>         Dear all,
> 
>         I am setting up a system with GROMACS 4.5.3 and the CHARMM force
>         field. In the protein, I have a neutral lysine, for which CHARMM
>         force
>         filed has a specific residue type (LSN). When I wrote LSN as residue
>         name in the initial pdb file, the topology file was perfectly
>         created
>         by pdb2gmx. However, in the next step, grompp complained about the
>         CMAP torsion between the two previous residues:
> 
>         Fatal error:
>         Unknown cmap torsion between atoms 2747 2749 2751 2754 2757
> 
>         However, if the LYS residue was written in the initial pdb file and
>         the -lys option included with pdb2gmx (chosen the neutral
>         protonation
>         state for this lysine), grompp did not complain.
> 
>         The problem is that there is a deprotonated tyrosine (bound to a
>         metal) in my system. I created a new residue type, but again the
>         grompp complained about the CMAP between the two previous residues.
>         Unfortunately, in this case I can't fit the problem with any of the
>         pdb2gms options.
>         I think the problem arises when a non-standard residue is
>         included in
>         the initial pdb file. Does someone else find this problem? I would
>         appreciate any advise about how to solve it.
> 
> 
>     I can't promise a solution, but you could try adding LSN and
>     whatever other non-standard residues you need to use in
>     residuetypes.dat.  I noticed that LSN is not there, which seems like
>     an omission, since the other CHARMM-specific residue names are
>     there.  When LYS is present, probably pdb2gmx is correctly
>     interpreting the residue as protein before converting its name.  In
>     the case of LSN or any other non-standard residue, this may not be
>     the case.  Check the output of pdb2gmx carefully for any messages
>     that might indicate that a residue of type "Other" was detected.
>      I've had this cause other problems.
> 
>     If adding LSN to residuetypes.dat fixes the problem, I will file a
>     bugzilla.
> 
>     -Justin
> 
>         Thanks in advance
> 
>         Jon
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
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> 

-- 
Dr Thomas Piggot
University of Southampton, UK.