Van der Waals Radii

Q:
I am writing about your article, The Packing Density in Proteins: Standard Radii and Volumes, published by JMB on 1999. In the article, in particular in table 2, you list a series of radii associated to each atom according to the number of hydrogens it has attached and a number you call the “valence”. However, valences of carbon are 2 and 4, and the list shows a valence 3 carbon; also valences for nitorgen are 3 and 5, and the tible shows a valence 4 one. Could you please explain what you mean by the term “valence” exactly? In particular, I am interested in knowing the type of heavy atoms you can find in glutamine and alanine residues, and their radii.

A:
Here, the term “valence” is perhaps best described in Table 1 (instead of Table 2). What is meant by the “n-term” (here, used synonymously with valence) is usually a geometric descriptor designating the orientation of other atomic species around that atom (for example, n=4 usually means that the atom builds a tetrahedron, whereas n=3 usually means that the atom is trigonal planar). Strictly speaking, and perhaps more accurately, n just designates the total number of atoms bound to a central atom. So, in your example of carbon’s n=3 in Table 2, these are carbon atoms which are connected to 3 other atoms (an example of C3H0 may be the carbonyl carbon in a protein backbone, and C3H1 may be a carbon atom in a phenyl group of PHE). In your example of nitrogen’s n=4, the N4H3 may represent the epsilon-amino group in LYS, since it is bound to 4 other atoms (one carbon and 3 hydrogen atoms).

problems in compilation of libproteingeometry-2-3-1

Q.
I am experiencing problems in trying to compile your package (libproteingeometry-2-3-1). I tried to compile it under Ubuntu-11.10 on a 32-bit VAIO centrino-based PC (gcc vers 4.6.1) and I got the following error message:

utypes.h:16:15: error: conflicting types for ‘float_t’
/usr/include/i386-linux-gnu/bits/mathdef.h:36:21: note: previous declaration of
‘float_t’ was here

Is it possible that this error is related CPPFLAGS settings?

I have also had difficulty compiling on an Intel i7 64-b machine under Ubuntu-11.10 with the same gcc version. This time the message was:

../src-lib/.libs/libproteingeometry: undefined reference to `sincos’ ../src-lib/.libs/libproteingeometry: undefined reference to `ceil’ ../src-lib/.libs/libproteingeometry: undefined reference to `atan2′ ../src-lib/.libs/libproteingeometry: undefined reference to `acos’ ../src-lib/.libs/libproteingeometry: undefined reference to `sin’ ../src-lib/.libs/libproteingeometry: undefined reference to `rint’ ../src-lib/.libs/libproteingeometry: undefined reference to `sqrtf’ ../src-lib/.libs/libproteingeometry: undefined reference to `pow’ ../src-lib/.libs/libproteingeometry: undefined reference to `sqrt’ ../src-lib/.libs/libproteingeometry: undefined reference to `floor’ collect2: ld returned 1 exit status

A.
This problem was resolved in a strange way. The package was compiled in the /usr/local dir of an Intel i5 machine, and all the compiled material was brought to the corresponding dir of an i7 computer. Almost the same had been done for a vaio 32-bit computer using a CD with the Ubuntu 9.10 version on another 32-bit system.

There may have been some collisions with environment flags set by the preceding compilation of other packages. In particular, Amber10 and Gromacs-4-5-5 had already been installed on the i7 and vaio.

morph server question

Q:

I am currently using your server to morph two actin structures (open nucleotide cleft and closed). Besides morphing the two actin chains, I would also like to morph the bound ATP molecules. Although I can the two actin structures to morph, I cannot seem to figure out how to morph the ATPs. So basically my question is: can bound nucleotides be morphed? How should they be defined in the PDB filem which server to use, and should the morphs be done separately (i.e. protein and ATP as separate morphs)?

A:

Thank you for your query, and for using MolMovDB. Specifically, which server is it that you have been using, and what error message(s) are returned? It is sometimes the case that the formatting of the PDB files must be manually changed in certain ways, and this in and of itself can be a little tricky. If you like (and if you don’t mind), you may send the PDB files to me, and I will spend some time on trying to format them for the server. If all else fails, it may indeed be necessary to morph things separately, but combining the resultant morphs may be an endeavor on its own.

Finally (and importantly), I should point out that the PDB formats may not be the issue at all; it may be the case that that there is an issue with ATP constituting ‘heteroatoms’. Dealing with heteroatoms in our server is extremely difficult, and this is sometimes a result of the way in which they’re numbered in your input files. In addition, parameterizing heteroatoms using our interpolation software is very difficult (to the point that, if you do indeed obtain a morph, the resultant interpolation may be very questionable, so it may be a use-at-your-own-risk practice if the parameterization is not done properly).