| General: |
Can I use these ports with both GROMACS v3.1.4 and v3.2.1?
Do these ports support dummy atoms? Why do all ports include atom names like either amber94_XX or amber99_XX? Why are there non-zero energy differences between the GROMACS ports and the AMBER 8.0 package? |
| pdb2gmx: |
Can I import pdb files with some or all hydrogens missing (-ignh flag)?
Why do LYS and CYS residues not follow standard residue nomenclature? Why does pdb2gmx keep trying to find "LYSH"? Why does pdb2gmx try to replace "LYS" with "LYN"? |
| grompp: |
Why do I get a grompp warning about missing ' characters?
Why do I get a grompp warning "missing white space after `#define proper_*'?" |
| Other: |
Why do I observe slight energy differences between this GROMACS port and the AMBER package
for a system containing TRP residues?
|
General:
Can I use these ports with both GROMACS v3.1.4 and v3.2.1?
Yes, but you must use the -H14 flag for pdb2gmx v3.1.4. This is now the default in v3.2.1 and the flag is not needed.
Do these ports support dummy atoms?
No. Dummy hydrogen parameters for proteins are not yet complete and dummy database (.ddb) files are not provided. We hope to have this feature implemented in the next version of the AMBER ports.
Why do all ports include atom names like either amber94_XX or amber99_XX?
The other ports are all variants of AMBER-94 (96, GS, GS-S) or AMBER-99 (99phi), and they were created from the validated AMBER-94 and AMBER-99 files respectively. These variants only change peptide phi/psi torsions, and it is convenient to maintain the atom names.
Why are there non-zero energy differences between the GROMACS ports and the AMBER 8.0 package?
There are two reasons. The first, as discussed below, is due to an inconsistency in the way AMBER orders improper torsions in TRP residues. This bug has been reported to the AMBER team, and our ports do not suffer from this issue. The second difference is seen in non-bonded interactions, which can have absolute values near zero. In these cases, the relative difference does not reflect the very low absolute error for these terms.
pdb2gmx:
Can I import pdb files with some or all hydrogens missing (-ignh flag)?
Yes and No. Protein ports have working hydrogen database (.hdb) files, so it is not necessary to have all-atom pdb models (i.e. including hydrogens). It is essential to copy aminoacids.dat to the top directory for this feature to work properly. For nucleic acids, all-atom pdb models are still needed (i.e. united atom models will need to be protonated ahead of time).
Why do LYS and CYS residues not follow standard residue nomenclature?
Why does pdb2gmx keep trying to find "LYSH"?
Why does pdb2gmx try to replace "LYS" with "LYN"?
This is due to a substring comparison in pdb2gmx that automatically renames any residues with names containing "LYS" or "CYS" with the "LYSH" and "CYS" nomers. Because of this hard coding, we cannot offer a simple work around to maintain the AMBER residue nomenclaure. As discussed on the website, renaming LYS residues to LYP (Lysine positive) in your .pdb file will get rid of these warnings and keep pdb2gmx from trying to use LYN (unprotonated Lysine neutral).
grompp:
Why do I get a warning about missing ' characters?
You can set "cpp = /lib/cpp -traditional" in your .mdp file to get rid of warnings about missing ' characters, which is due to the use of proper nucleic acid nomenclature, such as to distinguish between C4' and C4.
Why do I get a grompp warning "missing white space after `#define proper_*'?"
Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these warnings, which result from the use of the N* atom type of the AMBER family of force fields and can be ignored.
Other:
Why do I observe slight energy differences between this GROMACS port and the AMBER package for a system containing TRP residues?
This is due to a known bug in AMBER involving inconsistent ordering in an improper dihedral of TRP that has been reported. This is the cause of the non-zero mean dihedral energy difference for amino acids shown in the table on the port webpage, as all TRP systems have been included in these averages.
(c) 2005
Vijay Pande and Stanford University