[gmx-users] NMA problem
Dear All, I am using MM/PBSA to calculate protein-ligand binding affinnity using GROMACS. I got stuck at entropy calculation stage, which can be broadly done by two mthods i.e. Normal Mode Analysis and Quasi-Harmonic method. Can anyone let me know that how minimization using distance based dielectric (r-dielectric) with a prefactor of 4 can be done for normal modes calculation using GROMACS. Thanks in advance for any valuable suggeations. -- With Regards, Rashmi Kumari Research Scholar School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi- 110067. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] 1-4 Scaling problem of ASN-NAG from GLYCAM
Dear All, The protein on which I am working, have few ASN residues which are N-linked with the N-acetyl-glucosamine (NAG). I have taken the parameters of the NAG and N-linked ASN from the GLYCAM_06. I have added this N-linked ASN as a new residue in aminoacids.rtp file and accordingly all the parametrs are added in respective files. After this both pdb2gmx and grompp are working without any error. But the problem I am facing is related to 1-4 scaling. For the GLYCAM, fudgeLJ and fudgeQQ should be 1. I have read the following mailing post that how one can mix the fudgeLJ and fudgeQQ in GROMACS. http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html In the manual, I have come across with two type of pairs function. In function type 1, two parameters are needed and is used as default. But, in function type 2, five parameters are needed: fudgeQQ, q_i, q_j, V(cr) and W(cr). So can I replace function type 1 with 2 in the pdb2gmx generated topology for only those pairs belong to the NAG and side chains of N-linked ASN. So that, I can use fudgeQQ of 1.0, q_i / q_j from the rtp/topology and V(cr) / W(cr) (calculated from the sigma and epsilon using combination rule) for those pairs. Will this give No Scaling for 1-4 pair belong to NAG and side chains of N-linked ASN. Or another which I found “those 1-4 pairs belong to side chains of N-linked ASN and NAG, so I could remove them from [ pairs ] section and put into the [ pairs_nb ] section.” Then these pairs will be treated as normal non-bonded pairs. Please suggest me, what I can do in this regard and which is the correct way. Thank you in advance. -- With Regards, Rashmi Kumari Research Scholar School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi- 110067. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: extreme projections
Hi, If you have VMD installed, load the "extreme.pdb". Then in graphics> Representations--->Trajectory---> put values in "Draw Multiple Frames", for e.g. 0:10 this will show the extremes of 0th frame to 10th frame (you can change this a/c to your representation). After this selecting Draw style---> coloring method---> trajectory---> time step: this will help you to show the deviation in frames via different coloring. On Mon, Jul 15, 2013 at 5:12 AM, Ahmet yıldırım wrote: > any one please help me out with this problem? > > > 2013/7/10 Ahmet yıldırım > > > Dear users, > > > > I extracted separate extreme projections using g_anaeig. I have to make > > pictures which show the difference. Can you help me, someone who > makesthem using pymolbefore > > ? > > > > -- > > Ahmet Yıldırım > > > > > > -- > Ahmet Yıldırım > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Regards, Rashmi Kumari Research Scholar School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi- 110067. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2
Hi All, I want to install Gromacs 4.5.1 version on a cluster system (high performance computing facility) in our institute. I don't have access to root and thus, I have to install gromacs in my home directory. The problem is that, the cluster has CentOS 5.4 as the operating system and the gcc version is 4.1.2. Gromacs site says that gcc 4.1.x and above are broken compilers and gromacs should not be compiled using them. So I plan to install a compatible version of gcc, for eg. gcc-4.0.4, in my home directory and then install gromacs 4.5.1 using this compiler. Will this be ok? I am asking this question because the new gcc i will install will be compiled with the so called broken compiler version gcc 4.1.2 (which i cannot change). Is this the correct way to ensure that i do not compile gromcas with a broken compiler. Please do reply. Thanxs in advance. Rashmi IIT Bombay -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
