Saturday, March 1, 2014

Handling topologies of non-standard molecules in Gromacs

I have a file containing a protein chain and a non-standard ligand in a file [centered.pdb]. To obtain .top file
create a directory in the workspace and call it forcefield.ff.

export GMXLIB=$GMXLIB:$PWD/

The contents of that directory are:


ls -1 forcefield.ff/
aminoacids.c.tdb
aminoacids.hdb
aminoacids.n.tdb
aminoacids.r2b
aminoacids.rtp
aminoacids.vsd
atomtypes.atp
b12rtp
elements.dat
ffbonded.itp
ff_dum.itp
ffG53a6.itp
ffnonbonded.itp
forcefield.doc
forcefield.itp
gromos53a6.ff
ions.itp
old
org-aminoacidsrtp
spce.itp
spc.itp
tip3p.itp
tip4p.itp
watermodels.dat

The file aminoacids.itp has these lines added at the end:

[ Ligand ]
[ atoms ]
C27     C       0.38000 0 ; from        GLN     residue
O28     O       -0.38000 0 ; from       GLN     residue
N29     NT      -0.83000 0 ; from       GLN     residue
..

[ bonds ]
; ai aj gromos type
C26     C27 gb_27 ; from        GLN     fragment 0
C27     O28 gb_5 ; from GLN
C27     N29 gb_9 ; from GLN
...

[ dihedrals ]
; ai aj ak al gromos type
C3R     O2      P       O3 gd_20 ; from ADE     phosphate definition
C3R     O2      P       O3 gd_27 ; from ADE     phosphate definition
C2P     O3      P       O2 gd_20 ; from ADE     phosphate definition...





Then...

 pdb2gmx_sp -f centered.pdb  -o centered.pg.gro
...


 Select the Force Field:
From current directory:
 1: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
From '/usr/common/usg/gromacs/4.6.1-sp/share/gromacs/top':
 2: AMBER03 protein, nucleic AMBER94 (Duan et al.,.. 24, 1999-2012, 2003)
 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
...

16: [DEPRECATED] Encad all-atom force field, using full solvent charges
17: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
18: [DEPRECATED] Gromacs force field (see manual)
19: [DEPRECATED] Gromacs force field with hydrogens for NMR

Select 1 which is the forcefield contained in the directory forcefield.ff. This should run w/o errors and give a topol.top file. W/o editing topol.top running this code will give the following error;

grompp_sp -f min.mdp -c centered.pg.gro -p topol.top -o em.tpr
...

-------------------------------------------------------
Program grompp_sp, VERSION 4.6.1
Source code file: /global/homes/j/jdeslip/Builds/Hopper/gromacs-4.6.1/src/kernel/topio.c, line: 734

 Fatal error:
Syntax error - File ffnonbonded.itp, line 1
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
So, hide the first line and add the default gromos53a6.ff

;#include "./forcefield.ff/forcefield.itp"
#include "gromos53a6.ff/forcefield.itp"

That should let grompp run smoothly.


Posted by at

2 comments:

  1. otr214426September 9, 2014 at 4:24 AM

    INTERNATIONAL CONCEPT OF WORK FROM HOME
    Work from home theory is fast gaining popularity because of the freedom and flexibility that comes with it. Since one is not bound by fixed working hours, they can schedule their work at the time when they feel most productive and convenient to them. Women & Men benefit a lot from this concept of work since they can balance their home and work perfectly. People mostly find that in this situation, their productivity is higher and stress levels lower. Those who like isolation and a tranquil work environment also tend to prefer this way of working. Today, with the kind of communication networks available, millions of people worldwide are considering this option.

    Women & Men who want to be independent but cannot afford to leave their responsibilities at home aside will benefit a lot from this concept of work. It makes it easier to maintain a healthy balance between home and work. The family doesn't get neglected and you can get your work done too. You can thus effectively juggle home responsibilities with your career. Working from home is definitely a viable option but it also needs a lot of hard work and discipline. You have to make a time schedule for yourself and stick to it. There will be a time frame of course for any job you take up and you have to fulfill that project within that time frame.

    There are many things that can be done working from home. A few of them is listed below that will give you a general idea about the benefits of this concept.

    Baby-sitting
    This is the most common and highly preferred job that Women & Men like doing. Since in today's competitive world both the parents have to work they need a secure place to leave behind their children who will take care of them and parents can also relax without being worried all the time. In this job you don't require any degree or qualifications. You only have to know how to take care of children. Parents are happy to pay handsome salary and you can also earn a lot without putting too much of an effort.

    Nursery
    For those who have a garden or an open space at your disposal and are also interested in gardening can go for this method of earning money. If given proper time and efforts nursery business can flourish very well and you will earn handsomely. But just as all jobs establishing it will be a bit difficult but the end results are outstanding.

    Freelance
    Freelance can be in different wings. Either you can be a freelance reporter or a freelance photographer. You can also do designing or be in the advertising field doing project on your own. Being independent and working independently will depend on your field of work and the availability of its worth in the market. If you like doing jewellery designing you can do that at home totally independently. You can also work on freelancing as a marketing executive working from home. Wanna know more, email us on workfromhome.otr214426@gmail.com and we will send you information on how you can actually work as a marketing freelancer.


    Internet related work
    This is a very vast field and here sky is the limit. All you need is a computer and Internet facility. Whatever field you are into work at home is perfect match in the software field. You can match your time according to your convenience and complete whatever projects you get. To learn more about how to work from home, contact us today on workfromhome.otr214426@gmail.comand our team will get you started on some excellent work from home projects.


    Diet food
    Since now a days Women & Men are more conscious of the food that they eat hence they prefer to have homemade low cal food and if you can start supplying low cal food to various offices then it will be a very good source of income and not too much of efforts. You can hire a few ladies who will help you out and this can be a good business.

    Thus think over this concept and go ahead.

    ReplyDelete
  2. Retouching ZoneOctober 19, 2019 at 6:27 PM

    I really enjoyed your blog. Thanks!! for sharing such an informative post.
    Photo Editing Services | Architecture Photo Editing | Apparel Photo Editing

    ReplyDelete

Subscribe to: Post Comments (Atom)