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

[Shima Arasteh]

Again thanks for all your  replies.
As I got through your advices, I found that the atoms contribute in making bonds and angles in a residue , or make dihedrals in a residue ( or with atoms in next ones) plus the charge of a the residue should be defined properly in .rtp files to define the new residue in aminoacid.rtp file of CHARMM36 force field.
So I arranged this lines to define formyl in .rtp file. And I got the topology. But there are some questions for me here:

1. How can I be sure the formyl which I defined is correct? Is getting the topology is enough to be sure of the correct output?


The .rtp file for formyl is as below:
[ For ]
 [ atoms ]
;      name    type     charge   chargegroup
        C       CTL1     0.5700       0
        O       O       -0.5700       0
 [angles ]
  ai    aj    ak   
  O     C     +N 
 [ bonds ]
     C      O    
     C     +N
 
 [ dihedrals ]
  O     C   +N   +CA


2. There are lots of numbers in .itp file which I got through the swissparam.  But  I think the charge of atoms may be useful in this file and also I can just find the atoms contribute in bonds and angles and.... . Am I right? Or I may get some other useful information which I can get through the files of swissparam?

Thanks in advance, and sorry for disturbing you friends.

Shima



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


On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
>
>
> 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.
>

Another that I just caught as I hit send:

4. In your [bonds] and [angles] directives, you use atom numbers - they should 
be names

-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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