Re: [gmx-users] PDB file that can be read in Gromacs

As Justin has pointed out , this process is well documented and UNL is not often found in molecules. No matter what - you will have to do some leg work. Because I run into this almost daily, this may at least get you started. First try using x2top with a selected force field. If your

Re: [gmx-users] PDB file that can be read in Gromacs

Hi. First request, try to go through gromacs documentation and tutorials. You will get the clue. Topology of any nonprotein should be generated by a third party software or scripts depending on the forcefield. Have a detailed look into the tutorials. That will definitely help you. Thank you

Re: [gmx-users] PDB file that can be read in Gromacs

On 3/14/19 3:21 PM, Phuong Chau wrote: Hello everyone, I want to generate gromacs topology of a substance (a single chemical) which has a pdb file generated by RDKIT from SMILES representation of that substance (MolToPDBFile). However, when I input the pdb file generated by RDKit, it showed

[gmx-users] PDB file that can be read in Gromacs

Hello everyone, I want to generate gromacs topology of a substance (a single chemical) which has a pdb file generated by RDKIT from SMILES representation of that substance (MolToPDBFile). However, when I input the pdb file generated by RDKit, it showed the error of "Residue 'UNL' not found in

Re: [gmx-users] PDB file

On 8/15/16 9:30 AM, f.namazi...@sci.ui.ac.ir wrote: Hi Dear all; What are these columns "1.00" and "0.00" in PDB file? Google knows all about PDB format. -Justin for example: ATOM 10 N LEU A 2 4.595 6.365 3.756 1.00 0.00 N ATOM 11 CA LEU A 2

[gmx-users] PDB file

Hi Dear all; What are these columns "1.00" and "0.00" in PDB file? for example: ATOM 10 N LEU A 2 4.595 6.365 3.756 1.00 0.00 N ATOM 11 CA LEU A 2 4.471 5.443 2.633 1.00 0.00 C ATOM 12 C LEU A 2 5.841 5.176

Re: [gmx-users] *.pdb file for the Tip4p/ice model

04, 2016 8:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] *.pdb file for the Tip4p/ice model Since ice is a crystal, you can build a crystalline unit cell by hand (the unit cell will have one or two water molecules, so it's pretty easy to do it by hand, you just have

Re: [gmx-users] *.pdb file for the Tip4p/ice model

; > Sheelan S C > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Christopher > Neale [chris.ne...@alum.utoronto.ca] > Sent: Wednesday, March 30, 2016 11:25 PM > To: gmx-us...@gromacs.org > Subject: Re

Re: [gmx-users] *.pdb file for the Tip4p/ice model

: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sheelan Sengupta <s.sengu...@ncl.res.in> Sent: 30 March 2016 05:45 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] *.pdb file for the Tip4p/ice model need th

[gmx-users] *.pdb file for the Tip4p/ice model

need the *.pdb file of Tip4p/ice model. Please help. Regards, Sheelan S C Phys Chem Div Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory,

Re: [gmx-users] Pdb file

I mean potential energy of system (1600 argon atoms) is positive after energy mininization . On 12 Aug 2015 16:58, Vitaly V. Chaban vvcha...@gmail.com wrote: L_BFGS On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire ghimiresuni...@gmail.com wrote: I created the pdb file by genconf but the

Re: [gmx-users] Pdb file

L_BFGS On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire ghimiresuni...@gmail.com wrote: I created the pdb file by genconf but the system was not minimized, i got positive potential energy. What may be the problem? On 11 Aug 2015 19:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, gmx

Re: [gmx-users] Pdb file

Hello, I guess it is not unusual for gaseous systems to have positive energy. I hope that the Fmax criteria is satisfied. Sujith. On Wed, Aug 12, 2015 at 10:30 AM, Sunil Ghimire ghimiresuni...@gmail.com wrote: I mean potential energy of system (1600 argon atoms) is positive after energy

Re: [gmx-users] Pdb file

I created the pdb file by genconf but the system was not minimized, i got positive potential energy. What may be the problem? On 11 Aug 2015 19:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, gmx genconf on a small box with a single argon is a useful starting point. Mark On Tue, Aug

[gmx-users] Pdb file

How can i create the .pdb file for 1600 atoms of argon ? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] Pdb file

Hi, gmx genconf on a small box with a single argon is a useful starting point. Mark On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire ghimiresuni...@gmail.com wrote: How can i create the .pdb file for 1600 atoms of argon ? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] pdb file for united atom force fields

Dear Gromacs users, I need to work with a united atom FF, but I have defined all the Hydrogens in my pdb file. Does it cause any problem in MD procedure? Truly yours, Farideh -- Gromacs Users mailing list * Please search the archive at