Re: [gmx-users] 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations

That is very interesting. I once did QM/MM with Gaussian and am thinking of using gromacs. How can I register? Thanks, --- Robert Johnson <[EMAIL PROTECTED]> wrote: > Dear Colleague. > > We cordially invite you to register for attending > the: > > 2nd CMM 'Users Meet Developers' > Wo

Re: [gmx-users] coarse grain topology file

Just check very end of the top file. Make sure the numbers of sol, ions and TOTAL are consistent. --- Shanshan Qin <[EMAIL PROTECTED]> wrote: > Hi,everyone,I put forward the question yesterday. > When I run the simulation, the system always echo > "Fatal error: number of coordinates in coordinate

Re: [gmx-users] MD Error after adding a unnatural amio acid

tely. Or do you > mean charge > groups? Please try to be clear on such things. > Anyway, at this point the partial charges seem to be > the least of your > worries (unless you have a collection of -1,+1 or > worse stuck > together). I suspect your trouble is related to the >

[gmx-users] MD Error after adding a unnatural amio acid

Hi Everyone, I once talked about this before and have new problem now. The new group was successfully attached to the protein, but problem comes during the process of MD. The error messages are always like the following with either new linkage broken or a neighboring Hydrogen flying away. Paramete

Re: [gmx-users] Error when adding a unnatural amio acid

g. Thanks, Liu, Yuemin --- Yang Ye <[EMAIL PROTECTED]> wrote: > Please email me offline your pdb and rtp file. I > will see how to resolve > this issue. > > Regards, > Yang Ye > > On 1/4/2007 7:23 AM, yuemin liu wrote: > > This is a good idea. But here co

Re: [gmx-users] Error when adding a unnatural amio acid

l see how to resolve > this issue. > > Regards, > Yang Ye > > On 1/4/2007 7:23 AM, yuemin liu wrote: > > This is a good idea. But here comes following > major > > complaints: "Atom H4 not found in rtp database in > > residue ASO, it looks a bit like H1&quo

Re: [gmx-users] Error when adding a unnatural amio acid

cted to C4 and CBO. Atom type of O4 is OS which is sugar or ester oxygen, therefore no need H4 at all. So, what is likely the reason the program kept asking for H*? For better reference, large portion of the output is also give below. Thanks a lot, Yuemin Liu Opening library file ffgmx.rtp Openi

Re: [gmx-users] Error when adding a unnatural amio acid

ne > and decrement the > number on the top. > > Regards, > Yang Ye > > On 1/3/2007 11:18 PM, yuemin liu wrote: > > I did add the resname in aminoacids.dat and also > > change the the number on the top. It still > complains > > same thing. It is H at

Re: [gmx-users] Error when adding a unnatural amio acid

AIL PROTECTED]> wrote: > You may try add residue name ASO to the end of > /top/aminoacids.dat and > also increment the number on the top. > > Regards, > Yang Ye > > On 1/3/2007 8:55 AM, yuemin liu wrote: > > Hi, Everyone, > > > > I got Error when addin

Re: [gmx-users] Error when adding a unnatural amio acid

Thanks and Happy New Year! Wishes, Liu, Yuemin --- Yang Ye <[EMAIL PROTECTED]> wrote: > You may try add residue name ASO to the end of > /top/aminoacids.dat and > also increment the number on the top. > > Regards, > Yang Ye > > On 1/3/2007 8:55 AM, yuem

[gmx-users] Error when adding a unnatural amio acid

Hi, Everyone, I got Error when adding a unnatural amio acid in a protein. I have all the rtp and hdb file modified using information either from ffgmx.rtp ffgmx.hdb or thr rtp file form progdrg. There is no H1 in either rtp file or my new pdb file. When I try use pdb2gmx to generate top file, it a