You are right, CT1 is incorrect for sure. But the other option is C(carbonyl 
C) . Maybe I couldn't say it clearly. 
The FVAL which I sent before through mailing list, is the result of this 
formamide and the CGenff generation:
[ FVAL ]
>>     [ atoms ]
>>        CN    C    0.357    0
>>        ON    O    -0.51    1
>>        H1    HA    0.100    2
>>        N    NH1    -0.423    3
>>        HN    H    0.333    4
>>        CA    CT1    0.034    5
>>        HA    HB    0.09    6
>>        CB    CT1    -0.093    7
>>        HB    HA    0.09    8
>>        CG1    CT3    -0.268    9
>>        HG11    HA    0.09    10
>>        HG12    HA    0.09    11
>>        HG13    HA    0.09    12
>>        CG2    CT3    -0.268    13
>>        HG21    HA    0.09    14
>>        HG22    HA    0.09    15
>>        HG23    HA    0.09    16
>>        C    C    0.528    17
>>        O    O    -0.510    18
>>     [ bonds ]
>>        CN    H1
>>        CN    ON
>>        CN    N
>>        N    H
>>        CA    N
>>        CA    HA
>>        CA    C
>>        C    O
>>        CA    CB
>>        CB    HB
>>        CB    CG1
>>        CB    CG2
>>        CG2    HG21
>>        CG2    HG22
>>        CG2    HG23
>>        CG1    HG11
>>        CG1    HG12
>>        CG1    HG13
>>        
>>     [ impropers ]
>>      CN     N    ON    H1

This is the new residue which I defined and sent you(as remember), I used these 
parameters and atomtypes , and then went through mailing list and asked for 
your help a few days ago.
All over , with this procedure , I couldn't get the an acceptable result.


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 1:51 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up

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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