Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

Hi again. Thank you for your help I found my MANA in the ffG53a5.rtp and i can prepare the .gro and .top file from pdb2gmx. Now , i am facing another problem after solvation of my solute when i run the minimization the 1-6 linkage was broken .. please help me out thanks in

Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

Just a quick look at the ffG45a3.rtp shows that there is an entry for ADE, however the ADE entry is for Adenine. For help with your problem check out: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database Tom --On Friday, September 14, 2007 14:13:55

Re: [gmx-users] Topology builder

Erik Lindahl wrote: Hi, There are a couple of programs out there (e.g. Macromodel) that tries to do this, even for OPLS, but they fail miserably way too frequently. I've even seen cases where the autogenerated topology was reported as "likely high quality", but the small molecule didn't even

Re: [gmx-users] Topology builder

Hi, There are a couple of programs out there (e.g. Macromodel) that tries to do this, even for OPLS, but they fail miserably way too frequently. I've even seen cases where the autogenerated topology was reported as "likely high quality", but the small molecule didn't even have unit charge

Re: [gmx-users] Topology builder

> Dear Mark, > > The problem is a little bit more complicated. I want to build topologies > for > dozens of non-peptide inhibitor prototypes using OPLS FF. Thus, if there > is a > way to build this by an automatic procedure it would save much time. Well, if there was one, I might have mentioned it

Re: [gmx-users] Topology builder

> Hi, > > Is there any fast program to build topology for all-atom OPLS force-field? > I tried to use PRODRG, but it only has united atom possibilities. You must either use pdb2gmx or read Chapter 5 and gromacs/share/top/ffoplsaa* and produce one by hand. Mark ___

Re: [gmx-users] topology doesnt match

Robert Selwyne wrote: Dear GMX users When i tried to rum grompp i get these errors. Would any one be able to sort out this problem? Sincerely Robert - grompp -v -f adp.mdp -po adpmdout.mdp -c genbox.gr

RE: [gmx-users] topology doesnt match

Check if you have all group types in your mdp file. Ciao, Luciano Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938

Re: [gmx-users] Topology file for D2O

Hi, I am not an expert about heavy water -- but it does seem strange to me to think that you could get "heavy water" just by changing the mass of the hydrogens in a conventional water model. The *only* thing this will affect is the kinetic energy and mass of water. Presumably changing hydrogen to

Re: [gmx-users] Topology file for D2O

Hi Joys Yu, In addition to Tserks comments you might want to use a more specifically developed heavy water model. Here is a reference you may find usefull: An effective pair potential for heavy water - J. Raul Grigera The Journal of Chemical Physics -- May 8, 2001 -- Volume 114, Issue 18, pp. 8

Re: [gmx-users] Topology file for D2O

Hi Joys Yu, I'm not exactly sure what is happening and why the mass is not produced correctly. You could check in the .tpr file using gmxdump whether the masses are correct there, but given the log, it probably is not. It is possible that grompp does not read the altered ffgmx.atp, but uses an or

Re: [gmx-users] Topology Manipulation question

Hi! you usually get that type of output when the order in which the molecule atoms are written in the topology file (in the itp in your case) does not correspond to the order in the gro file; it might just be that you call the itp corresponding to the second molecule written in the gro file before

Re: [gmx-users] Topology question

Anthony Cruz wrote: Hi users: I made a small molecule topology using the PRODRG topology generation server but I want to use it with the G43a1 GROMOS96 43a1 Forcefield. How I could change the parameters from GROMACS to GROMOS??? thanks Anthony __

Re: [gmx-users] topology transformation

Anthony Cruz wrote: Hi users: Hi Anthony, How I can convert a topology generated by PRODRG topology generation server to a gromos topology??? or I cant use it with the G43a1 GROMOS96 43a1 Forcefield did you try the beta version? It generates 43A1 topologies. There are some issues with

Re: [gmx-users] topology transformation

Anthony Cruz wrote: Hi users: How I can convert a topology generated by PRODRG topology generation server to a gromos topology??? or I cant use it with the G43a1 GROMOS96 43a1 Forcefield There is no automatic way to do that. You'll have to assign Gromos atom types (which are similar to

Re: [gmx-users] topology database

Dhananjay wrote: Hello all, while pdb2gmx on my pdb I got following error --- Program pdb2gmx, VERSION 3.3 Source code file: resall.c, line: 438 Fatal error: Residue 'MSE' not found in residue topology database Will it be possible to add

Re: [gmx-users] Topology database

Dhananjay wrote: Hello all, while pdb2gmx on my pdb I got following error --- Program pdb2gmx, VERSION 3.3 Source code file: resall.c, line: 438 Fatal error: Residue 'MSE' not found in residue topology database Will it be possible to add

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