[gmx-users] Number of SOL/Water in gmx_moltype_t

, *nr=1*, ic=' '} Aren't we recording the number of solvent residues? I was expecting nr=351 for SOL; the number of water molecule I have in the system. As I get nr=2 for OHN Thanks, Pradip Biswas -- P. K. Biswas, PhD Laboratory of Computational Biophysics Bioengineering Associate Professor

Re: [gmx-users] Number of SOL/Water in gmx_moltype_t

that there are 351 of those molecules recorded. The same is true of the DNA chain, but since there's only one DNA chain, the number of residues per molecule coincides with the number in the system. Mark On Tue, Aug 20, 2013 at 7:48 PM, Pradip Biswas biswas...@gmail.com wrote: Hi, I am using v

[gmx-users] do we still have a do_dssp and dssp compatibility issue? thread: do_dssp failed to execute

I encountered the exact same error with Gromacs-4.5 as posted by Sunita Patel back in October 2010 and could not find any solution in the gmx_thread. The error was: Failed to execute command: /home/path-to-dssp -na dd3sOJn3 ddZl9dcf /dev/null 2 /dev/null I found that the do_dssp fails to fork

Re: [gmx-users] qmmm linking atom

Which QM method in Gromacs are you using? On Tue, May 10, 2011 at 5:41 PM, Yao Yao ya...@ymail.com wrote: Hi gmxers, I am just wondering how to give a linking atom's coordinates in a qmmm calculation generally. Would it be normal to take an arithmetic average of two neighboring

Re: [gmx-users] multiplicity for qmmm simulations

Hi Jorge, Sorry, I missed you mail earlier. As per the distributed qmmm version, part of the QM information are being fed through the Gromacs mdp file and part through the CPMD_inp.tmpl file. Please specify your QM charge and multiplicity in the CPMD_inp.tmpl file. P.Biswas On Sun, Oct 24,

Re: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS)

Thanks for the info. pb. On Mon, Dec 14, 2009 at 11:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Pradip Biswas wrote: Hi, The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM

Re: [gmx-users] Problem with Gromacs-CPMD

Hi Jorge, I'll appreciate if you can send me (biswas...@gmail.com) the following files if the problem still persists: 1. output.mdrun_em 2. qm_cpmd.log Also please let me know which version of CPMD you are using. best, pb. On Thu, Nov 19, 2009 at 1:59 PM, jorge_quint...@ciencias.uis.edu.co

[gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS)

Hi, The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM, these oxygen atoms are being recognized as Nitrogen atoms. Biswas. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] typo for opls_179 (OS) and opls_180 (OS) in ffoplsaanb.itp

Hi, Just noted that the oxygen atom types defined in opls_179 and opls_180 have atomic numbers typed in as 7 in ffoplsaanb.itp instead of 8 (the mass numbers are okay 15.9994 though). Accordingly, while doing QMMM, these oxygen atoms are being recognized as Nitrogen atoms. Biswas. -- Pradip K

[gmx-users] Extended structure for Estrogen receptor

Dear All, All the estrogen receptor alpha structure that I found on PDB repository, contain mainly the ligand binding domain (residues 301-550). I am looking for a structure that has the hinge region (240-300) as well. Does anyone have any extended structure (even if it is an engineered one) of

Re: [gmx-users] Extended structure for Estrogen receptor

Justin, I came to this board as a last resource, after failing in my search. Pradip On Wed, Oct 7, 2009 at 9:09 AM, Justin A. Lemkul jalem...@vt.edu wrote: Pradip Biswas wrote: Dear All, All the estrogen receptor alpha structure that I found on PDB repository, contain mainly the ligand

[gmx-users] option for finding forces between two groups

Hi, Anyone can please tell me whether there is any option in GROMACS to find forces between two groups (say for example, between two residues in a protein or between a peptide and a residue in a Protein for Protein-peptide interaction) or one need to workaround with the code to get that? Thanks

Re: [gmx-users] Problems with metals GROMACS/CPMD

Hi, This error has origin in the Gromacs part of the QMMM interface. If you can send me the index.ndx, .gro, and CPMD_inp.run files, I might figure out what's going on. -pb. On Fri, Sep 11, 2009 at 11:38 AM, jorge_quint...@ciencias.uis.edu.cowrote: Hello all. I have tried to perfomed some

Re: [gmx-users] CPMD- QM MM simulation

Hi Christian, Thanks for your idea. I'll start writing up a short manual to make it available in the QMMM website in the near future. Meanwhile, it will be great if you and other users can contribute to this manual by writing up small pieces mentioning the difficulties you faced and how you

Re: [gmx-users] QMMM

I believe it supports GAMESS UK, not US. Gerrit ([EMAIL PROTECTED]) can assist you further. pb On Mon, Aug 25, 2008 at 4:30 AM, ha salem [EMAIL PROTECTED] wrote: hello I want install gromacs with gamess US for QMMM can you guide me for installation procedure thank you

[gmx-users] New Gromacs-CPMD QMMM webpage

Dear Users, The modified Gromacs code for Gromacs-CPMD QMMM is now available at: http://www.tougaloo.edu/research/qmmm/ Please note that we fixed a bug related to MM layering in the version gmx-3.3.1_qmmm-1.3.1 and uploaded a new version, gmx-3.3.1_qmmm-1.3.2. If you are using version 1.3.1, you