[gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

[Shima Arasteh]

Thanks for your suggestions.


The total charge is zero in real but what I got through swissparam is as below:
[ atoms ] 
; nr type resnr resid atom cgnr charge mass 
   1 C=O  1  LIG C       1  0.4500  12.0110 
   2 O=C  1  LIG O       2 -0.5700  15.9994 
   3 HCMM 1  LIG H1      3  0.0600   1.0079 
   4 HCMM 1  LIG H2      4  0.0600   1.0079 

So I entered as I showed you.

In addition how can I add the proton on it? Editing the C to CT1 is right? or I have to add any charge here?

Formyl is connected to valine in the peptide sequence in this .pdb file. Now, what about adding  this line ?:  

[ dihedrals ]
  O     C   +N   CA 


Cheers,
Shima


________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, May 12, 2012 10:07 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs
 


On 5/12/12 1:32 PM, Shima Arasteh wrote:
> Dear gmx users,
>
> I want to simulate a peptide in water. The peptide has a formyl residue as the
> N-terminus. I got the parameters of it and then add it to the .rtp file of
> charmm36.ff as below:
>
> [ For ]
> [ atoms ]
> ; name type charge chargegroup
> C C 0.4500 0
> O O -0.5700 0
> [ bonds ]
> ; ai aj fu b0 kb, b0 kb
> 1 2 1 0.12220 779866.6 0.12220 779866.6
>
> [ pairs ]
> ; ai aj fu
>
> [ angles ]
> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
> 2 1 3 1 123.4390 403.48 123.4390 403.48
> 2 1 4 1 123.4390 403.48 123.4390 403.48
>
> [ dihedrals ]
> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
>
> But when I do what I described, I face this fatal error:
> Fatal error:
> No atoms found in .rtp file in residue
 pairs
>
> Would you help me with this problem? Did I add the formyl in a wrong way?
>

Your [pairs] directive is empty, hence the error.  Your [dihedrals] directive 
will also produce the same error.  There are no possible pairs in a unit 
containing so few atoms, so you don't even need this.  You may need to define 
dihedrals, however, but they also depend upon the next residue.

You also have several other mistakes:

1. A formyl group has a proton on it; yours has none
2. Your net charge on the formyl group is not zero, though this may or may not 
be a consequence of point #1
3. There is no connectivity information for linking to the next residue, which 
will mean the formyl group will not be chemically bonded.  This also affects 
your dihedrals.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Department of
 Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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