Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
On 2012-11-18 10:40, Atila Petrosian wrote: Dear David Thanks for your attention. I have 2 problems/questions: 1) There are a specific orientation for GLN ligand with regard to protein in my system. If I do what you said [you make a separate molecule Gln-Ala using pymol or vmd], specific orientation for GLN ligand with regard to protein are changed. no since you only use the procedure for the topology creation. 2) topology obtained from NGLN-CALA is as follows: [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 GLN rtp NGLN q +1.0 1 N3 1GLN N 1 0.1493 14.01 ; qtot 0.1493 2 H 1GLN H1 2 0.1996 1.008 ; qtot 0.3489 3 H 1GLN H2 3 0.1996 1.008 ; qtot 0.5485 4 H 1GLN H3 4 0.1996 1.008 ; qtot 0.7481 5 CT 1GLN CA 5 0.0536 12.01 ; qtot 0.8017 6 HP 1GLN HA 6 0.1015 1.008 ; qtot 0.9032 7 CT 1GLN CB 7 0.0651 12.01 ; qtot 0.9683 8 HC 1GLNHB1 8 0.005 1.008 ; qtot 0.9733 9 HC 1GLNHB2 9 0.005 1.008 ; qtot 0.9783 10 CT 1GLN CG 10-0.0903 12.01 ; qtot 0.888 11 HC 1GLNHG1 11 0.0331 1.008 ; qtot 0.9211 12 HC 1GLNHG2 12 0.0331 1.008 ; qtot 0.9542 13 C 1GLN CD 13 0.7354 12.01 ; qtot 1.69 14 O 1GLNOE1 14-0.6133 16 ; qtot 1.076 15 N 1GLNNE2 15-1.0031 14.01 ; qtot 0.0732 16 H 1GLN HE21 16 0.4429 1.008 ; qtot 0.5161 17 H 1GLN HE22 17 0.4429 1.008 ; qtot 0.959 18 C 1GLN C 18 0.6123 12.01 ; qtot 1.571 19 O 1GLN O 19-0.5713 16 ; qtot 1 ; residue 2 ALA rtp CALA q -1.0 20 N 2ALA N 20-0.3821 14.01 ; qtot 0.6179 21 H 2ALA H 21 0.2681 1.008 ; qtot 0.886 22 CT 2ALA CA 22-0.1747 12.01 ; qtot 0.7113 23 H1 2ALA HA 23 0.1067 1.008 ; qtot 0.818 24 CT 2ALA CB 24-0.2093 12.01 ; qtot 0.6087 25 HC 2ALAHB1 25 0.0764 1.008 ; qtot 0.6851 26 HC 2ALAHB2 26 0.0764 1.008 ; qtot 0.7615 27 HC 2ALAHB3 27 0.0764 1.008 ; qtot 0.8379 28 C 2ALA C 28 0.7731 12.01 ; qtot 1.611 29 O2 2ALAOC1 29-0.8055 16 ; qtot 0.8055 30 O2 2ALAOC2 30-0.8055 16 ; qtot 0 You said Then you edit the top file (remove superfluous alanine atoms, rename the N in ALA to O2 etc) with a text editor until it is correct with help from the rtp file for CGLN. You may have to smooth the charges to keep it neutral In ALA residue, all atoms except for N are redundant atoms. After removing them and renaming N in ALA to O2, what remains in top file? Both of NGLN and CALA or only NGLN? If latter is true, [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 GLN rtp GLN q 0.0 1 N3 1GLN N 1 0.1493 14.01 ; qtot 0.1493 2 H 1GLN H1 2 0.1996 1.008 ; qtot 0.3489 3 H 1GLN H2 3 0.1996 1.008 ; qtot 0.5485 4 H 1GLN H3 4 0.1996 1.008 ; qtot 0.7481 5 CT 1GLN CA 5 0.0536 12.01 ; qtot 0.8017 6 HP 1GLN HA 6 0.1015 1.008 ; qtot 0.9032 7 CT 1GLN CB 7 0.0651 12.01 ; qtot 0.9683 8 HC 1GLNHB1 8 0.005 1.008 ; qtot 0.9733 9 HC 1GLNHB2 9 0.005 1.008 ; qtot 0.9783 10 CT 1GLN CG 10-0.0903 12.01 ; qtot 0.888 11 HC 1GLNHG1 11 0.0331 1.008 ; qtot 0.9211 12 HC 1GLNHG2 12 0.0331 1.008 ; qtot 0.9542 13 C 1GLN CD 13 0.7354 12.01 ; qtot 1.69 14 O 1GLNOE1 14-0.6133 16 ; qtot
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[gmx-users] Force vs distance plot in pulling simulation?
But be aware that the force depends on the pulling velocity. If you perform the simulation with two different pulling velocities you'll get two different forces for each distance. The easiest way to get the force as a function of the distance (without the bias of the pulling velocity) would be thermodynamik intergration. This is similar to the umbrella sampling. You set up some windows with different distances. But instead of restraining the distance with an umbrella potential (as in umbrella sampling) you use a constraint to fix the distance and than can determine the constraint force. Greetings Thomas Am 17.11.2012 16:44, schrieb gmx-users-requ...@gromacs.org: Hi Erik and Justin Thanks, writing such a script is easy. The point of it all would be to be able to map the magnitude of the pulling force to what I see happen in the pulling simulation. How else would you get an understanding of what the pulling force means? Thanks /PK The only solution is to write a simple script that parses out the columns you want. -Justin I don't see the point though. Except for checking implementation of the pull code. -- 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] Temperature Histogram
Thank you for your answer. However, when I use g_energy on .edr file it prints the average temperature of the system and not of the group of atoms that I am interested in, which is why I was trying to make g_traj work cos it uses index.ndx file for choosing the segment from your system and calculate the average temperature for that segment. One more thing, g_energy has Pres-XX, XY etc., what are these? Cheers, Nino From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, November 14, 2012 2:18 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Temperature Histogram On 11/14/12 7:10 AM, Samadashvili Nino wrote: Dear Justin, I have been looking for some option to calculate the average temperature, locally in my system. I found g_traj which I can use with index file and calculate temperature for a particular group in my system but somehow it gives a wrong value (The average temperature (NVT simulation) is 240 K and g_traj outputs 120 K). Is there any other option available in Gromacs? g_traj doesn't account for constraints, but the result can be calculated from what g_traj produces. That's more complicated than you need, and will not be accurate over all MD steps. All you need to do is extract the temperatures from the .edr file using g_energy and the average is printed to the screen. This average is correct over all steps, since energy history is stored in the .edr file and is not limited to nst* output. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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
