Re: [gmx-users] pdb file error

Thanks. Sylwia - Oryginalna wiadomość - Od: "Justin Lemkul" Do: "Discussion list for GROMACS users" Wysłane: środa, 22 sierpień 2012 14:56:16 Temat: Re: [gmx-users] pdb file error On 8/22/12 8:48 AM, Sylwia Chmielewska wrote: > Thank you for your prompt rep

Re: [gmx-users] pdb file error

within the manual. Beyond that, even Google searching will turn up useful results within seconds. -Justin Best Regards Sylwia - Oryginalna wiadomość - Od: "Justin Lemkul" Do: "Discussion list for GROMACS users" Wysłane: środa, 22 sierpień 2012 13:50:11 Temat: Re:

Re: [gmx-users] pdb file error

Wysłane: środa, 22 sierpień 2012 13:50:11 Temat: Re: [gmx-users] pdb file error On 8/22/12 7:44 AM, Sylwia Chmielewska wrote: > Hello, > > I'm new in Gromacs. I'm using gromacs 4.5.3. I need help with pdb format. I > use to convert my file by PRODRG and MN.CONVERT. > I&#x

Re: [gmx-users] pdb file error

On 8/22/12 7:44 AM, Sylwia Chmielewska wrote: Hello, I'm new in Gromacs. I'm using gromacs 4.5.3. I need help with pdb format. I use to convert my file by PRODRG and MN.CONVERT. I'm trying to create a topology file from the pdb using the pdb2gmx. I get an error. My molecules are quaternary a

[gmx-users] pdb file error

Hello, I'm new in Gromacs. I'm using gromacs 4.5.3. I need help with pdb format. I use to convert my file by PRODRG and MN.CONVERT. I'm trying to create a topology file from the pdb using the pdb2gmx. I get an error. My molecules are quaternary ammonium salts. My pdb file by MN. CONVERT: HEADER

Re: [gmx-users] pdb file of polymer

thanx a lot Justin for reply Regards parvez On Fri, Jun 29, 2012 at 2:27 PM, Justin A. Lemkul wrote: > > > On 6/29/12 2:21 PM, Parvez khan wrote: >> >> Hi, I am trying to do polymer simulation with gromacs. I am new to >> gromacs and trying to construct topology for a system of polymer >> chains

Re: [gmx-users] pdb file of polymer

On 6/29/12 2:21 PM, Parvez khan wrote: Hi, I am trying to do polymer simulation with gromacs. I am new to gromacs and trying to construct topology for a system of polymer chains. My problem is that i am facing difficulties to creat pdb file for polymer chain containing 1000 monomers. I have use

[gmx-users] pdb file of polymer

Hi, I am trying to do polymer simulation with gromacs. I am new to gromacs and trying to construct topology for a system of polymer chains. My problem is that i am facing difficulties to creat pdb file for polymer chain containing 1000 monomers. I have used PRODRG server but it gives me a pdb and t

[gmx-users] pdb file

: [gmx-users] pdb file A neat way to get generic coordinates of organic molecules like this is using Jmol: 1) go to http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?USESIGNED     This requires Sun/Oracle Java plugin activated in the browser and asks for permission to trust the signed applet

Re: [gmx-users] pdb file

from your response. > > Best Regards > Dina > > > From: Justin A. Lemkul > To: dina dusti ; Discussion list for GROMACS users > > Sent: Monday, March 12, 2012 10:02 PM > Subject: Re: [gmx-users] pdb file > > > > dina dusti wrote: >> Dear Gr

[gmx-users] pdb file

Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul To: dina dusti ; Discussion list for GROMACS users Sent: Monday, March 12, 2012 10:02 PM Subject: Re: [gmx-users] pdb file dina dusti wrote: > Dear Gromacs Speciali

Re: [gmx-users] pdb file

dina dusti wrote: Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? There are numerous methods for produ

[gmx-users] pdb file

Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? Please help me. Thanks in advance. Best Regards Dina -- gmx-

Re: [gmx-users] .pdb file for DNA

You can try also 3DNA: http://rutchem.rutgers.edu/~xiangjun/3DNA/ Regards Paulo A. Netz On Mon, Mar 7, 2011 at 3:40 AM, majid hasan wrote: > Dear All, > > I want to simulate interaction between single strand dna and cnt. I tried > to use Biomer (from case group webpage), but it's not work

Re: [gmx-users] .pdb file for DNA

Not really that Gromacs-related, but: In Ambertools, there's a program called nab(?) a.k.a. nucleic acid builder which performs that task very well. Sequence in, pdb-structure out, also for DNA single strands and RNA. Regards, Alex > Dear All, > > I want to simulate interaction between single s

[gmx-users] .pdb file for DNA

Dear All, I want to simulate interaction between single strand dna and cnt. I tried to use Biomer (from case group webpage), but it's not working. When I try to open B.html in my browser, I get a blank page. Could anyone please tell me if there is another way to generate .pbd file for dna? Th

Re: [gmx-users] pdb file problem

benrezkallah djamila wrote: Hello Everybody; I have a problem with The 2PU3 pdb entry (download from www.rcsb.org ) ; the download file gives for certain residues such as residu 25 : SER (and others in the pdb file), two different positions for the atoms of the residu.

RE: [gmx-users] pdb file

s to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of leila karami > Sent: Friday, 6 August 2010 11:00 PM > To: gmx-users > Subject: [gmx-users] pdb file > > Hi gromacs users > > I obtained p

Re: [gmx-users] pdb file

leila karami wrote: Hi gromacs users I obtained pdb input file for gromacs from STRAP program. this pdb file coantains protein and dna. this pdb file was obtaind form superposition of 2 other pdb files. there is one problem: when I see pdb file obtained from STRAP program by VMD, some bonds ar

Re: [gmx-users] pdb file

I opened your file in the molecular viewer Chimera and it displayed all the bonds. Molecular viewers have different ways of estimated if atoms are bonded or not. Hope it helps. --- Lucio Montero PhD Student Insituto de Biotecnologia, UNAM, Mexico. El vie, 0

Re: [gmx-users] pdb file

On 06/08/10 13:59, leila karami wrote: Hi gromacs users I obtained pdb input file for gromacs from STRAP program. this pdb file coantains protein and dna. this pdb file was obtaind form superposition of 2 other pdb files. there is one problem: when I see pdb file obtained from STRAP program by V

[gmx-users] pdb file

Hi gromacs users I obtained pdb input file for gromacs from STRAP program. this pdb file coantains protein and dna. this pdb file was obtaind form superposition of 2 other pdb files. there is one problem: when I see pdb file obtained from STRAP program by VMD, some bonds are disappeared whereas wh

Re: [gmx-users] pdb file for CNT

neo lotus wrote: Hi How pdb file for CNT is made? Have a look at the following: http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Bi

[gmx-users] pdb file for CNT

Hi How pdb file for CNT is made? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send i

[gmx-users] pdb file for ammonia

Hi Nisha, Hetero-Atom Navi is a collection of heteroatoms culled from the PDB. http://hetpdbnavi.nagahama-i-bio.ac.jp/index.php?mode=0 However, having only one heavy-atom, ammonia is unlikely to be usefully extracted from this resource for use in atomistic MD. You can easily make it yourself

RE: [gmx-users] pdb file for ammonia

It is easy to make one yourself. I would use molden to draw ammonia and save as pdb file. You might need to minimize before using for md. Abu > Date: Thu, 31 Dec 2009 16:21:29 -0500 > From: nishap.pa...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users]

Re: [gmx-users] pdb file for ammonia

nishap.pa...@utoronto.ca wrote: Does anyone know where I can get a pdb file for ammonia? I tried searching but I am not sure if there is a website for the pdb files I can use in gromac. Any suggestions would be helpful. For something simple like ammonia, you could probably just write the c

[gmx-users] pdb file for ammonia

Does anyone know where I can get a pdb file for ammonia? I tried searching but I am not sure if there is a website for the pdb files I can use in gromac. Any suggestions would be helpful. Thanks. Nisha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listi

Re: [gmx-users] pdb file

leila karami wrote: my pdb file for dna and protein contains 640 and 1130 atoms respectively. if I want creat a new pdb file for studying pr-dna interaction, should be numbering and order of numbers changed? how? Numbering is the least of your worries, generating a reasonable starting str

[gmx-users] pdb file

my pdb file for dna and protein contains 640 and 1130 atoms respectively. if I want creat a new pdb file for studying pr-dna interaction, should be numbering and order of numbers changed? how? ___ gmx-users mailing listgmx-users@gromacs.org http://lis

[gmx-users] pdb file

my pdb file for dna and protein contains 640 and 1130 atoms respectively. if I want creat a new pdb file for studying pr-dna interaction, should be numbering and order of numbers changed? how? ___ gmx-users mailing listgmx-users@gromacs.org http://lis

Re: [gmx-users] pdb file badly broken after changing residue name a/c to amber.rtp file

nitu sharma wrote: Dear justin I am trying to do simulation of dna-protein complex . For this I am using amber port with gromacs-4.0.3 but for this a/c to ffamber.rtp file entry i hqve to make changes in my .pdb file residues like the DNA base name in this is only A

[gmx-users] pdb file badly broken after changing residue name a/c to amber.rtp file

Dear justin I am trying to do simulation of dna-protein complex . For this I am using amber port with gromacs-4.0.3 but for this a/c to ffamber.rtp file entry i hqve to make changes in my .pdb file residues like the DNA base name in this is only A ,C ,G,T so a/c to amber.r

Re: [gmx-users] pdb file and force filed

Bhawana Gupta wrote: Hello sir, From last few days , i was using TINKER for implicit simulations using force field oplsaa Now for explicit one, i switched to gromacs version 4.0.But if i take pdb file from tinker (molecular modelling software) and paste it in The Dundee Prodrg server. i got

Re: [gmx-users] pdb file and force filed

Hello, For usual peptides having amino acids you need not use Dundee Prodrg server. pdb2gmx itself will generate the required .itp and .gro files. If u were using opls force fiels in tinker then use the same force fields in gromacs also because atom types are defined in different ways in different

[gmx-users] pdb file and force filed

Hello sir, >From last few days , i was using TINKER for implicit simulations using force field oplsaa Now for explicit one, i switched to gromacs version 4.0.But if i take pdb file from tinker (molecular modelling software) and paste it in The Dundee Prodrg server. i got my *.itp file, *.gro file.

Re: [gmx-users] pdb file

He, Yang wrote: Hi all users, I just encountered a problem about the DNA model when I set the coordinate in the pdb file . It always shows very strange figure about the DNA model. My pdb file is like this: ATOM 1 Ab1 DNA 1 0.0510.575 0.516 1.0 0.0 ATOM 2 Tb1

[gmx-users] pdb file

Hi all users, I just encountered a problem about the DNA model when I set the coordinate in the pdb file . It always shows very strange figure about the DNA model. My pdb file is like this: ATOM 1 Ab1 DNA 1 0.0510.575 0.516 1.0 0.0 ATOM 2 Tb1 DNA 1 0.1

Re: [gmx-users] pdb file ???

Hi Lin, If you include bromide, you won't have excess charge... So, no need for adding more counterions. Cheers, Tsjerk On Thu, Aug 21, 2008 at 8:20 AM, Chih-Ying Lin <[EMAIL PROTECTED]> wrote: > Hi > It is the water-molecule system. > For a molecule, like R-N(CH3)3-Br, I could make a pdb fil

[gmx-users] pdb file ???

Hi It is the water-molecule system. For a molecule, like R-N(CH3)3-Br, I could make a pdb file either include Br ion or exclude Br ion. If I exclude Br ion, I have to make Br ion as the counter ion for my system. If I include Br ion, I do NOT have to make Br ion as the counter ion since it will

Re: [gmx-users] pdb file from prodrg2 cannot be recognized by gromacs?

Hi, You need to get the topology file from PRODRG together with the PDB file so you skip pdb2gmx and use the outputs from PRODRG in grompp directly. Of cource, do whatever you need to add water and ions before grompp. Regards, Yang Ye On 9/5/2007 10:51 AM, Yafei Dai wrote: I got a pdb file

RE: [gmx-users] pdb file from prodrg2 cannot be recognized by gromacs?

> I was told "DRG" not found in residue topology. What can I do > for this error information? My pdb file is as below: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_ residue_topology_database Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and

Re: [gmx-users] pdb file from prodrg2 cannot be recognized by gromacs?

Yafei Dai wrote: I got a pdb file from prodrg2 and I did pdb2gmx: pdb2gmx -f test.pdb -p test.top -o test.gro I was told "DRG" not found in residue topology. What can I do for this error information? My pdb file is as below: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_foun

[gmx-users] pdb file from prodrg2 cannot be recognized by gromacs?

I got a pdb file from prodrg2 and I did pdb2gmx: pdb2gmx -f test.pdb -p test.top -o test.gro I was told "DRG" not found in residue topology. What can I do for this error information? My pdb file is as below: REMARK REMARK REMARK This file was generated by PRODRG version 061128.0522 REMARK

Re: [gmx-users] pdb file of a crystal lattice of epoxy resin

vijay kumar wrote: can any one send me a format of pdb file of epoxy resin,i want to simulate just epoxy resin crystal lattice cubic box size of 12 am and distance between each cube is 6 am using boundary temperature pdb file of epoxy resin CH2CHO (cubic structure) total of 8 lattices if possible

[gmx-users] pdb file of a crystal lattice of epoxy resin

can any one send me a format of pdb file of epoxy resin,i want to simulate just epoxy resin crystal lattice cubic box size of 12 am and distance between each cube is 6 am using boundary temperature pdb file of epoxy resin CH2CHO (cubic structure) total of 8 lattices if possible topology file and st