[gmx-users] Diagnosing + system blowing up

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jul 30 11:21:42 CEST 2012

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.
> 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.


> Sincerely,
> Shima
> ----- Original Message -----
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at 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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