On 1/4/16 8:20 AM, masoud keramati wrote:
in OPLS ff when i use tip3p water i got this error but if tip3p selected
then there no problem and it's interesting!
This comment makes no sense. Changing water models (presumably that is what you
mean, and just typoed it) will not work unless you re-solvate the system.
TIP3P, TIP4P, and TIP5P all have different numbers of atoms, hence there will
certainly be a mismatch with the topology if you simply try to change the water
model when running genbox.
-Justin
On Mon, Jan 4, 2016 at 2:18 PM, Justin Lemkul <[email protected]> wrote:
On 1/4/16 4:27 AM, soumi wrote:
Respected Sir,
I am new user of gromacs. When I use the following command
gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr
I get the following error :Number of coordinates in coordinate file does
not match topology file.
Please tell me how can I correct the number of coordinates in gromacs?
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
Since you've (presumably) already solvated the system, you probably forgot
to let genbox adjust your topology for you via the -p option. Based on
your file naming, I assume you're following my lysozyme tutorial, which
lays everything out exactly, so be sure you're using the exact commands and
you know what each option is doing.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to [email protected].
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to [email protected].
