maria goranovic wrote:
Hi
I am using editconf to set my box to the right size using:
editconf -f in.gro -o out.gro -box 30 30 30
gromacs v. 4.5.3
For this example, my system contains a phosphate anion and a water
molecule. After editconf runs, it changes the residue name SOL of the
water molecule to the residue name PHO for phosphate, because both have
the same residue number (1). Is this not a bug, or am I doing something
really silly? One can always try to run a simulation of an amino acid in
water, and the error below would be replicated?
I suspect so. You can file a bug report, but it will probably remain a very low
priority for now. One normally does not number a coordinate file this way.
Each residue should be numbered independently.
Interestingly, grompp does not complain that the residue PHO has 8 atoms
instead of 5 as in the topology file.
AFAIK grompp only pays attention to atom names, which in this case likely match
the topology without an issue.
-Justin
I do not see this problem if the residue number of the water molecule is
2 instead of 1.
Below are the two .gro files, before and after running the above command.
GROtesk MACabre and Sinister
8
1PHO O1P 1 13.422 2.753 5.900
1PHO P 2 13.250 2.818 5.976
1PHO O2P 3 13.193 2.967 5.853
1PHO O3P 4 13.263 2.864 6.169
1PHO O4P 5 13.118 2.672 5.939
1SOL OW 1 12.025 1.421 -1.203
1SOL HW1 2 12.125 1.421 -1.203
1SOL HW2 3 11.993 1.516 -1.203
20 20 20
GROtesk MACabre and Sinister
8
1PHO O1P 1 15.623 15.449 17.622
1PHO P 2 15.451 15.514 17.697
1PHO O2P 3 15.394 15.663 17.574
1PHO O3P 4 15.464 15.560 17.890
1PHO O4P 5 15.319 15.368 17.660
1PHO OW 6 14.226 14.117 10.518
1PHO HW1 7 14.326 14.117 10.518
1PHO HW2 8 14.194 14.212 10.518
30.00000 30.00000 30.00000
--
Maria G.
Technical University of Denmark
Copenhagen
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
