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#33962 - 05/21/14 02:12 AM Adding Graphene to the Residue Topology File
Hinshelwood Offline
Forum Member

Registered: 04/04/14
Posts: 2
Loc: US
I have been attempting to write a RTF file to include a graphene residue and keep getting the following error.

Code:
***** LEVEL  2 WARNING FROM <RTFRDR> *****
      ***** Atoms were missing in the last improper torsion. Ignored.
      ******************************************
      BOMLEV (  0) IS NOT REACHED. WRNLEV IS  5

          IMPR -CGG1 -CGG2 -CGG3 -CGG4 -CGG5 -CGG6 CGG1 CGG2 CGG3 CGG4 CGG5 CGG
          6 +CGG1 +CGG2 +CGG3 +CGG4 +CGG5 +CGG6
 There were    1 error(s) from RTFRDR.
 Execution will be terminated.


Here is the section of the RTF I have added for graphene. If anyone sees mistakes causing the error I would appreciate it if you could point them out. Also, I have not been able to find a lot of documentation on the IMPR command its syntax usage etc.

Code:
! Begin graphene mass desgination
MASS   222 CGG1  12.01100 C ! C for graphene
MASS   223 CGG2  12.01100 C ! C for graphene
MASS   224 CGG3  12.01100 C ! C for graphene
MASS   225 CGG4  12.01100 C ! C for graphene
MASS   226 CGG5  12.01100 C ! C for graphene
MASS   227 CGG6  12.01100 C ! C for graphene

DECL -CA  
DECL -C  
DECL -O  
DECL +N  
DECL +HN  
DECL +CA
DECL -CGG1
DECL -CGG2
DECL -CGG3
DECL -CGG4
DECL -CGG5
DECL -CGG6
DECL +CGG1
DECL +CGG2
DECL +CGG3
DECL +CGG4
DECL +CGG5
DECL +CGG6
!nucleic acid section
DECL  +P
DECL  +O1P
DECL  +O2P
DECL  +O5'
DECL  -O3'

DEFA FIRS NTER LAST CTER   
AUTO ANGLES DIHE

RESI GRAPHENE		0.00
ATOM CGG1   CGG1	0.00
ATOM CGG2   CGG2 	0.00
ATOM CGG3   CGG3 	0.00
ATOM CGG4   CGG4 	0.00
ATOM CGG5   CGG5 	0.00
ATOM CGG6   CGG6 	0.00
!
!    CGG1--CGG2
!    //      \\
!  CGG3      CGG4
!     \  __  /
!    CGG5--CGG6
! 
AROMATIC CGG1 CGG2 CGG3 CGG4 CGG5 CGG6
IMPR -CGG1 -CGG2 -CGG3 -CGG4 -CGG5 -CGG6 CGG1 CGG2 CGG3 CGG4 CGG5 CGG6 +CGG1 +CGG2 +CGG3 +CGG4 +CGG5 +CGG6


Attachments
graphene_topall27_prot_na.txt (526 downloads)
Description: complete rtf file



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#33965 - 05/21/14 08:44 AM Re: Adding Graphene to the Residue Topology File [Re: Hinshelwood]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4755
Loc: ~ 59N, 15E
The AROMATIC and IMPR statements are NOT just lists of atoms. They specify connectivity, so the number of atoms listed and their order is IMPORTANT.

AROMATIC does not have any special meaning to CHARMM (it is the same as BOND). Your AROMATIC statement only specifies three bonds (and CGG3 CGG4 does not seem correct). Is that really what you want?
The IMPRoper statement is also strange. An improper torsion is defined by 4 atoms (see rtop.doc and parmfile.doc), and it is maybe clearer if you just list one improper on each line, eg:
IMPR A B C D
IMPR E F G H
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#33967 - 05/21/14 10:46 AM Re: Adding Graphene to the Residue Topology File [Re: Hinshelwood]
Kenno Offline
Forum Member

Registered: 12/19/05
Posts: 1535
Loc: Baltimore, MD
This whole approach appears deeply flawed on many levels and will likely never work. Can you go back a few steps and tell us exactly what system you want to simulate and what existing force field you want to use for it?

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#33991 - 05/31/14 03:55 PM Re: Adding Graphene to the Residue Topology File [Re: Hinshelwood]
Hinshelwood Offline
Forum Member

Registered: 04/04/14
Posts: 2
Loc: US
I'd like to simulate the adsorption of insulin to graphene using the charmm22 potential and TIP3P water model. The above rtf file represents how I was attempting to add graphene into charmm. I understand how the IMPR/AROMATIC command works from lennart's post. How would you approach this?

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#33997 - 06/04/14 10:21 AM Re: Adding Graphene to the Residue Topology File [Re: Hinshelwood]
Kenno Offline
Forum Member

Registered: 12/19/05
Posts: 1535
Loc: Baltimore, MD
First of all, it is recommended to use the newer CHARMM36 potential instead.

Then, let me explain why your approach won't work. the polymerization features in CHARMM's RTF format are mostly convenient for 1D polymers; crosslinking and branching are usually implemented in the form of patches. For a 2D graphene sheet of relevant size, you'll need to apply so many patches that it will negate the advantage of the "polymer" approach altogether. In other words, I think you'll be better off generating the graphene sheet as one monolithic residue. The easiest way to do so starting from a mol2 file is the attached script. Please do heed the limitations listed at the beginning of the file.

Note that the script
  • uses existing atom types (specifically CG2R61 from CGenFF, though it would work just as well with CA from the CHARMM protein force field). We recommend against introducing new atom types unless (1) you really know what you're doing and (2) have a really good reason. (1) is obviously violated in your case since you attempted to define different atom types for chemically equivalent atoms. (There are a few exceptional cases where that's worth doing, but graphene isn't one of them, and even if it were, 6 atom types would still be far too many.)
  • will not generate IMPR statements. The reason for this is that 6-membered aromatic rings in CHARMM do not benefit from improper dihedrals; the out-of-plane behavior is adequately captured by the angle and (proper) dihedral potential alone and impropers would only over-rigidify them. See also this FAQ entry.
  • defines all the bonds by BOND entries; as Lennart mentioned, "AROMatic" doesn't have any special meaning to CHARMM.


Finally, assuming you're using PBC, IF you want an infinite graphene sheet that spans the periodic boundary, then things get a bit more complicated and you'll still need patches. I'm not experienced enough to be able to tell for sure how to best accomplish this; the other forum regulars may know more.


Attachments
graphene_mol2rtf.awk.txt (504 downloads)


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