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 <jalem...@vt.edu
<mailto:jalem...@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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