[gmx-users] How to treat CSD residue in protein

Hi all, I am having a protein, contains CSD instead of cysteine in active site, ligating with Zn ion. Is it right to replace residue CSD with Cysteine and connect it with Zn ion through covalent bond explicitly or to make special topology for CSD ? Please reply me. With thanks! B.Nataraj -- raj

Re: [gmx-users] norleucine topology

i used the amberGS ff from the amber gromacs ports. hdb and rtp entries are attached. On Sunday 20 August 2006 13:38, David van der Spoel wrote: > merc mertens wrote: > > dear list, > > > > to get a topology for norleucine i combined parameters from LEU (N,CA,CB, > > plus H´s, C, O) and MET (CG,

Re: [gmx-users] Is there any bug in gromacs v3.3 g_order analysis tool?

Dear Prof. Spoel, Many thanks for your prompt reply. It has solved my problem. But I have a doubt, if that is the case then everytime it should report 5 frames missing only, why then in some cases it reports 10 frames missing while in others 50 missing frames? regards, Priyanka. --- David van de

Re: [gmx-users] editconf

editconf -h editconf -translate ... cat xxx.pdb >> yyy.pdb and remove the TER and ENDMDL lines Good luck, Jochen mahbubeh zarrabi wrote: Dear gmx_users I am trying to insert one alpha-helical peptide . I created two pdbs, bilayer.pdb and peptide.pdb . how can i were adjusted the peptide c

Re: [gmx-users] editconf

Why not copy the coordinates of the channel in to th lipid's file? Itamr. mahbubeh zarrabi wrote: Dear gmx_users I am trying to insert one channel peptide in lipid bilayer. I created two pdbs, bilayer.pdb and peptide.pdb . how can i were adjusted the peptide coordinates using editconf to be

[gmx-users] SWM4-DP (Roux group polarizable water model) .itp file needed

Hello, Does anyone on the list have a .itp file for the recent Roux group SWM4-DP polarizable water molecule model? DvS mentioned a couple of months back that recent polarizable water molecule models from this group, and also models from the van Gunsteren group [presumably COS(G?)] work in GR

[gmx-users] editconf

Dear gmx_users I am trying to insert one channel peptide in lipid bilayer. I created two pdbs, bilayer.pdb and peptide.pdb . how can i were adjusted the peptide coordinates using editconf to be at the desired vertical position in the bilayer. thanks

Re: [gmx-users] Is there any bug in gromacs v3.3 g_order analysis tool?

priyanka srivastava wrote: Dear gromacs users, I am doing a lipid-bilayer simulation using gromacs 3.3 version. While calculating the order parameters, although I am having a hard time. When I issue the following command: g_order -f lb.trr -s lb.tpr -n sn2.ndx -b 0 -e 30 I get the following o

Re: [gmx-users] RMSD

Dhananjay wrote: The starting structure is a homology model. (If you need some more details then please tell me) well that explains it probably, the starting structure is not a good protein structure. you can use the MD to tell you why the model falls apart. force field : GROMOS96 43a1

[gmx-users] Is there any bug in gromacs v3.3 g_order analysis tool?

Dear gromacs users, I am doing a lipid-bilayer simulation using gromacs 3.3 version. While calculating the order parameters, although I am having a hard time. When I issue the following command: g_order -f lb.trr -s lb.tpr -n sn2.ndx -b 0 -e 30 I get the following output: trn version: GMX_trn_

[gmx-users] editconf

Dear gmx_users I am trying to insert one alpha-helical peptide . I created two pdbs, bilayer.pdb and peptide.pdb . how can i were adjusted the peptide coordinates using editconf to be at the desired vertical position in the bilayer. thanks __ D

Re: [gmx-users] RMSD

The starting structure is a homology model.  (If you need some more details then please tell me) force field :  GROMOS96 43a1 I have not at all added or removed any ion manually. amount of water : using  genboc -cs ( spc216.gro ) water is added.  Here the details are as follows Reading sol

Re: [gmx-users] RMSD

Dhananjay wrote: Hello all, I am running mdrun for a system of protein having 182 residues. (Before going for MD, mdrun for EM and PR has been done as per the instructions given in the online manual.) After 3ns job is over, I calculated RMSD and it is about 0.6 nm. This is too high. I

[gmx-users] Re: gmx-users Digest, Vol 28, Issue 63

org/mailman/listinfo/gmx-users > 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/mailing_lists/users.php > -- next part -- An HTML attachment was scrubbed..

[gmx-users] RMSD

Hello all, I am running mdrun for a system of protein having 182 residues. (Before going for MD,  mdrun for   EM and PR  has been done as per the instructions given in the online manual.)  After 3ns job is over, I calculated RMSD and it is about 0.6 nm.  This is too high. In the mailing list, m

Re: [gmx-users] periodic boundary condition

yes, they are sufficient. if I remember well, the flag -pbc does the opposite job, it removes periodic boundary conditions. anyway, remember to include in your mdp file the parameters for the treatment of periodic bonudary conditions!   regards,   Maria  On 8/21/06, [EMAIL PROTECTED] <[EMAIL PROTE

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