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. <br><br>The DPPC is defined in terms of two more residues in CHARMM.<br>
<br>amit<br><br><div class="gmail_quote">On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
Jon Mujika wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear all,<br>
<br>
I am setting up a system with GROMACS 4.5.3 and the CHARMM force<br>
field. In the protein, I have a neutral lysine, for which CHARMM force<br>
filed has a specific residue type (LSN). When I wrote LSN as residue<br>
name in the initial pdb file, the topology file was perfectly created<br>
by pdb2gmx. However, in the next step, grompp complained about the<br>
CMAP torsion between the two previous residues:<br>
<br>
Fatal error:<br>
Unknown cmap torsion between atoms 2747 2749 2751 2754 2757<br>
<br>
However, if the LYS residue was written in the initial pdb file and<br>
the -lys option included with pdb2gmx (chosen the neutral protonation<br>
state for this lysine), grompp did not complain.<br>
<br>
The problem is that there is a deprotonated tyrosine (bound to a<br>
metal) in my system. I created a new residue type, but again the<br>
grompp complained about the CMAP between the two previous residues.<br>
Unfortunately, in this case I can't fit the problem with any of the<br>
pdb2gms options.<br>
I think the problem arises when a non-standard residue is included in<br>
the initial pdb file. Does someone else find this problem? I would<br>
appreciate any advise about how to solve it.<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
If adding LSN to residuetypes.dat fixes the problem, I will file a bugzilla.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks in advance<br>
<br>
Jon<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><br>
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