On 30/07/2012 7:11 PM, Shima Arasteh wrote:
In CHARMM36 folder, there is a atomtypes.atp that I chose the atomtypes of
formyl group ( as you see earlier)
No, I saw atom types chosen that included wrong things like CT1. If
you're happy that you're using atom types that belong in formyl, then go
and do the rest of the investigative procedure I suggested for the
bonds/angles/dihedrals. I'm not going to write it again!
. If I don't use these, so what atom types?!
I sent an email to Prof.Roux the author of this article
http://www.pnas.org/content/101/1/117.abstract . He suggested me to use the
parameters of formamide the charmm36.rtf file .
RESI FORM 0.00 ! CH3NO formamide, adm jr.
GROUP
ATOM HA HGR52 0.08 !
ATOM C CG2O1 0.42 ! O Hc
ATOM N NG2S2 -0.69 ! \\ /
ATOM HC HGP1 0.35 ! C--N
ATOM HT HGP1 0.35 ! / \
ATOM O OG2D1 -0.51 ! HA Ht
I found something similar to what I used here for my defined formyl group.Would
this be useful?
Potentially a good start, but you will have to decide how to deal with
the charge distribution, because you need to replace Ht with the rest of
valine and end up with a neutral charge distribution that makes sense.
One approach is to define a residue (based on those atom types and
charges) with just formyl, since the above fragment has HC(O)- that is
almost neutral. You can then proceed with using normal valine after that.
Mark
Sincerely,
Shima
----- Original Message -----
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Cc:
Sent: Monday, July 30, 2012 1:22 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
On 30/07/2012 6:36 PM, Shima Arasteh wrote:
Thanks dear Mark.
Actually the atomtype C is more suitable for C atom of formyl and not CT1!
The same as before I get the no default bonds/angles/dihedral errors . You
explained what I am suppose.
I can understand the way of matching the coordinate file and atom types in .rtp
file. But it's not clear for me that what I am supposed to check? bonds? I
don't know what I need to do.
Your .rtp entry has to specify atom types. Those atom types have to make
chemical sense. Then there have to be bond/angle/dihedral parameters for all
the combinations you want to use. It may be that this is impossible (and
pdb2gmx is having trouble, which suggests this is true), but you can't know
without looking at the force field files. This is about the third time I've
said to go looking for formyl atom types in atomtypes.atp. They're probably not
there. Atom types for HC(O)N(H)R... are almost certainly not there, and they
are what you really want, and they'd be quite different from HC(O)R formyl
anyway.
If I look for the bonds/dihedrals and then don't find them, what's the next
step?
Search the literature to see if anyone else has used this functional group, but
probably give up and use acetyl, like everybody else does. You have to have a
compelling reason to want to bother to parameterize this group, and I'd suggest
you get a lot more experience first.
Mark
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