Research:amber tips
Renumber xyz/pdb file
If you want to renumber xyz file, e.g. delete a molecule from the old xyz, you can manually remove the lines for these atoms. However, you cannot manually modify the pdb in the same way by deleting the ATOM and CONNECT entries. It will cause trouble running amber later on. (Well, no error msg would be printed out, but it stops right before the first step). The correct way is to convert xyz to pdb with xyzpdb command.
FEP-vdw
During the FEP, you cannot make any of the vdw parameters zero. Although it might not give you error message at the beginning, it will cause trouble in running sander later on. The error messege is usually "Input conversion error", and you will see NaN in prmtop file.
truncated octahedron
From http://structbio.vanderbilt.edu/archives/amber-archive/2005/2439.php
Here is the source code where the Volume of the bounding cube is multipled by 0.7698004 in tools.c:
dVolume = dMaxX * dMaxY * dMaxZ;
if ( bOct ) (Yes in this case)
dVolume *= 0.7698004; /* = sqrt(1 - 3*cost^2 - 2*cost^3),
where cost = -1/3 = cos(109.471) */
VP0(( " Volume: %5.3lf A^3 %s\n", dVolume, (bOct ? "(oct)" : "") ));
http://www.gromacs.org/documentation/reference_3.2/online/editconf.html
asserts this constant (.77) as well....
I don't have a quick reference on the trigonometry, unfortunately.
amber archive: http://dev-archive.ambermd.org/200707/0008.html
> In amber, the box information is defined with 6 values; > > 51.9046302 51.9046302 51.9046302 109.4712190 109.4712190 109.4712190 > > and as far as I understood, each of the first 3 values are the half of a > cube's edge length (l/2; assuming we have a cube with edge length of 'l'). > From these 6 parameters, someone needs to find what 'a' is.
No, the actual lengths of the periodic unit cell are there, not 1/2 the box length. If orthorhombic (i.e. rectangular with 90 degree angles), these are the lengths of each side of the box.
> I do not understand what 109.4712190 is. In your explanation, u define a
This is the angle between the sides; as an example, use ptraj to image your truncated octahedron without specifying the "familiar" keyword. It will look like a slanted rectangle. The angles are all 109.47... between each side.
> parameter 'a' which is not clear to me. It is not the edge length of a > truncated octahedron defined in the above website.
Do not trust the above mentioned website :-)
You can look through the ptraj or sander or PMEMD code and see:
V = x * y * z * sqrt(1.0 - cos(alpha)**2 - cos(beta)**2 - cos(gamma)**2 +
2.0 * cos(alpha) * cos(beta) * cos(gamma))
x, y, z are the box lengths: x = y = z = a in your example. alpha, beta, gamma are the box angles which equal 109.47... for a truncated octahedron.
An easier shape (since the angles are integral and hence do not suffer from finite precision) which we haven't exploited in AMBER is the rhombic dodecahedron (12-sided, equal sides) which has x=y=z and alpha=60, beta=90, gamma=60). This is the shape that is closest to a sphere, yet space filling.
We discuss this in Current Protocols in Nucleic Acid Chemistry (articles by Cheatham, Kollman and Brooks) from ~2000-2003. See the attached PDF for a summary.
From: Thomas Cheatham <tec3.utah.edu>
Date: Thu Jul 26 2007 - 12:26:55 PDT
> octahedron" can be defined in multiple ways....". Do u mean that in a > different space where you have a different type of metric, the 'truncated > octahedron' can be defined different? Or do u mean that the volume of a > 'truncated octahedron' can be defined in multiple ways?
What I mean is that it can be implemented in different ways and hence how to determine its volume will differ. In Allen & Tildesley, there is an algorithm that implements a truncated octahedral geometry. This is not equivalent to the triclinic/AMBER definition. LEaP used to be able to produce this "other" kind of box.
> > V = x * y * z * sqrt(1.0 - cos(alpha)**2 - cos(beta)**2 - cos(gamma)**2 + > > 2.0 * cos(alpha) * cos(beta) * cos(gamma)) > > > > > Another question is, why to use triclinic cell? Is it hard to explicitly > use truncated octahedrals in the simulations? By combining triclinic > cells, someone can create a continous system; but this must be true for > combining truncated octahedrons, too.
The triclinic is a general property that fits well within the PME framework. Those other boxes in that previous table map to the triclinic. The standard Allen & Tildesley could map, but it would require a different orientation of the box and different definition of the "length of a side".
> Unfortunately, our library does not have this journal. Can u give me the > full references of these papers published in this journal? I will ask from > the library to get it for me, but they need the full reference > information. Thanks again.
What I would worry about understanding is the box_to_recip() code in PME/AMBER, PMEMD, sander, or ptraj. This will allow you to better understand the box. If the angle is 109.47 it IS a truncated octahedron / it is also a particular triclinic shape.
--tom
p.s. you may have Current Protocols in the lab there...
Current Protocols in Nucleic Acid Chemistry:
(20) T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. "Molecular modeling of nucleic acid structure" in Current Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.5.1-7.5.13 (1999).
(25) T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. "Molecular modeling of nucleic acid structure: Energy and sampling" in Current Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.8.1-7.8.21 (2001). (26) T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. "Molecular modeling of nucleic acid structure: Electrostatics and solvation" in Current Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.9.1-7.9.22 (2001). (27) T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. "Molecular modeling of nucleic acid structure: Setup and analysis" in Current Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.10.1-7.10.18 (2001). Received on Sun Jul 29 06:07:26 2007
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Sander troubleshooter
"mismatch in line"
When you see this error in your amoeba_parm.out, that's sign your atom type for the ligand is not correct.
Could be due to the grouping after average.
Some atoms should have the same type somehow still carry the old type which does not exist in parameter file
Another possible reason is that polarizability and charge are both 0 at the same time. Make charge 0.000001 in tinker prm would help (otherwise tinker delete this atom from the array). It would affect the answer because analyze will only print out 0.00000 with 1 trunctaed.
Careful with H's vdw
You always need the third value for vdw parameter as long as it's defined as H. Even if you are at the last step of turning H off. Or in Amber, it will die the first step with NaN temperature