Re: [gmx-users] GLUH problem

Dear Jason, I am trying to use pdb2gmx to generate files for my molecules. I have protonated GLU in it. So I am using GLUH as the residue name. However the program complains that Fatal error: Atom HE2 in residue GLU 4 not found in rtp entry with 10 atoms while sorting atoms.

[gmx-users] GLUH problem

Dear all: I am trying to use pdb2gmx to generate files for my molecules. I have protonated GLU in it. So I am using GLUH as the residue name. However the program complains that Fatal error: Atom HE2 in residue GLU 4 not found in rtp entry with 10 atoms while sorting atoms. Maybe

[gmx-users] pull code question

 Dear GMX users, I am simulating the hydrophobic interaction between two 42-aminoacid oligopeptides in pbc conditions with acqueous explicit solvent with all-bonds constraints (LINCS).  In order to allow them to interact -for the first time- I am using pull code.   My pull.ppa is as follows

Re: [gmx-users] Restraining bilayer/water system

The posre itp file represents one lipid molecule and the p2.itp file represents all water molecules. I have a p1.itp file that represents one water molecule but this also brought up the : cpp exit code: 256 cpp: too many input files [tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I -I/u

Re: [gmx-users] Restraining bilayer/water system

You shall append those three lines just under the definition of the lipid molecule. You may paste your top file for us to comment. Yang Ye Farid Sa'adedin wrote: Dear Users, I have been trying to equilibrate a bilayer. I have been able to restrain a bilayer in its own system using #ifdef

Re: [gmx-users] Re: LINCS Warning using mdrun

Grazia Daminelli wrote: Dear Jochen what do you mean with: Better show us the output of your energy minimization. The ouput of your md only shows that your sctructure has some serious problem...like your box is too small or whatever... Jochen which term is telling you that there are prob

[gmx-users] Restraining bilayer/water system

Dear Users, I have been trying to equilibrate a bilayer. I have been able to restrain a bilayer in its own system using #ifdef POSRES #include "/home/tripos/lipid/dopc/minidopc/posre.itp" #endif in the topology file define = -DPOSRES in the steep, nvt and npt mdp files. The problem occurs

Re: [gmx-users] Not enough ref_t and tau_t values

Thanks TsjerkYes, there was a non-standard amino acid residue and it was not recognising it as part of the protein. I changed the total number of residues in the aminoacid.dat file (which I had not!) and then everything worked ok.AshutoshOn Mar 16, 2006, at 3:09 AM, Tsjerk Wassenaar wrote:Hi Ashuto

[gmx-users] Re: [gmx-developers] REMD based on prot pot ener: FINAL?

hi, pascal Would you like to take a look at this recent articles on JCTC? http://dx.doi.org/10.1021/ct050196z @article{OkurA._ct050196z, author = {Okur, A. and Wickstrom, L. and Layten, M. and Geney, R. and Song, K. and Hornak, V. and Simmerling, C.}, title = {Improved Efficiency of Replica Ex

Re: R: R: [gmx-users] Dihedral restraints

You may consider to use following to get the latest 3.3. cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx Yang Ye STEVENAZZI ANDREA wrote: Dear David I am desperate actually and would appreciate a lot

Re: [gmx-users] How to make drug for OPLSA ff compatiable

Sorry, no. I never worked on hemes or whatever FE is included. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mg

Re: [gmx-users] need suggestion for building TMA

Hi, I would consider to try to use the program genconf in Gromacs. With this program you can stack and multiply a given coordinate file "like a small child playing with wooden blocks" - Gromacs manual. Mikko Hellgren PhD student at Karolinska Institutet [EMAIL PROTECTED] Message: 3 Date: Wed,

Re: [gmx-users] How to make drug for OPLSA ff compatiable

Thanks Mr. Goette, But error list is not so long , its simple as Fatel error: atom type 'CR61' not found in the topology , where 'CR61' is the atom type occurs first in my drug itp file made from PRODRG. Otherwise could you suggest me any other forcefield otherthan OPLSA to treat Fe(II) in active

Re: [gmx-users] How to make drug for OPLSA ff compatiable

You simply can't do that, right now. OPLS isn't implemented into PRODRG, yet (correct me, if I'm wrong). Therefore the atom-naming, etc. maybe wrong. Anyway...a more detailed documentation of the error would be very helpful. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical

Re: [gmx-users] Not enough ref_t and tau_t values

Hi Ashutosh, If no index file is explicitly given to grompp, it will use default index group (as if you did echo q | make_ndx -f test_b4pr.gro -o index.ndx) Grompp does not know of definitions given in the .top file with regards to the groups. Does your protein contain some non-standard residues?

Re: [gmx-users] Not enough ref_t and tau_t values

On Wed, 15 Mar 2006 17:21:52 -0600 Ashutosh Jogalekar <[EMAIL PROTECTED]> wrote: I know this question has been discussed a number of times on the list, but almost everytime it has been discussed in reference to the index file. I am getting this error during grompp for the position restrained

R: R: [gmx-users] Dihedral restraints

Dear David I am desperate actually and would appreciate a lot if you could send me the dihres.c that works with version 3.2. Just in case is not so clear how to add the right lines in the topology file by reading the code would you please suggest it to me too? Thanks a lot Best regards Andrea A