Dear Justin,
Thanks for your valuable helps. How should I rearranged the conf.gro file
for 6 EDO ligand? is the following conf.gro mistake?
*conf.gro:*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
5354
2GLN N 1 1.458 -1.158 0.739
2GLN H1 2 1.520 -1.083 0.763
...
485HOH HW1 5333 0.221 -3.864 -2.291
485HOH HW2 5334 0.303 -3.946 -2.407
1EDO OAB 1 0.625 -3.071 -0.171
1EDO HAA 2 0.698 -3.048 -0.107
1EDO CAA 3 0.596 -3.211 -0.163
1EDO CAC 4 0.486 -3.247 -0.261
1EDO OAD 5 0.365 -3.179 -0.224
1EDO HAB 6 0.292 -3.203 -0.288
1TRS O1 1 1.825 -3.900 0.047
1TRS HAA 2 1.853 -3.860 -0.040
1TRS C1 3 1.712 -3.977 0.028
1TRS C 4 1.659 -4.044 0.150
1TRS C3 5 1.576 -3.946 0.226
1TRS O3 6 1.634 -3.824 0.256
1TRS HAC 7 1.569 -3.768 0.307
1TRS N 8 1.582 -4.159 0.113
1TRS HAE 9 1.547 -4.204 0.195
1TRS HAF 10 1.505 -4.131 0.056
1TRS HAD 11 1.639 -4.223 0.062
1TRS C2 12 1.776 -4.085 0.233
1TRS O2 13 1.887 -4.122 0.160
1TRS HAB 14 1.961 -4.148 0.222
8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550 0.00000
0.00000 0.00000
14 Nisan 2011 20:15 tarihinde Justin A. Lemkul <jalem...@vt.edu> yazdı:
>
>
> ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> I built .rtp entries for two ligands using (
>> http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top the
>> following parts:
>> #include "TRS.itp"
>> #include "EDO.itp"
>>
>
> Well, either pdb2gmx built the molecules into your topology or you're
> #including them in this manner, you should not do both.
>
> TRS 1
>> EDO 6
>>
>
> So this is part of your [molecules] directive? If you've got six copies of
> EDO, that's likely where the disconnect comes from - you only had one in
> your previous coordinate file snippet.
>
>
> Furthermore I added the number of atoms (20) in the second line of the
>>
>
> If you have 6 EDO, the necessary addition is more than just 20.
>
>
> .gro file. may the problem related to pdb file (3NM4.pdb)? Because -OH
>> groups seems as -O. isn't it? maybe I'm wrong. What would you recommend?
>>
>>
> Generally H atoms are not present in crystal structures. If your ligands
> require certain H atoms, then you must do one of two things:
>
> 1. Add all the necessary hydrogen atoms to the protein and ligands and run
> pdb2gmx.
>
> 2. Have no H atoms present in the initial coordinate file and build
> suitable .hdb entries for your ligands so they will be constructed from
> existing atoms.
>
> It seems like you're applying several different methods at once. There are
> protein-ligand tutorials that you may find useful for keeping all of this
> straight (I recommend my own):
>
> http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems
>
> -Justin
>
> 2011/4/14 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>> ahmet yıldırım wrote:
>>
>> Dear users,
>>
>> pdb2gmx -f xxx.pdb
>> water:spc
>> forcefield:43a1
>> editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
>> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
>> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>> *Fatal error:*
>> number of coordinates in coordinate file (solvated.gro, 106523)
>> does not match topology (topol.top, 106553)
>> I look at gmx-user search. But I dont be able to solved the
>> problem. Then I look at conf.gro and box.gro. I recognised the
>> there is not the TRS ligand in the box.gro file. What reason?
>>
>>
>> Based on your workflow, it looks as is you never added it in. If
>> conf.gro came from pdb2gmx, did you build .rtp entries for your
>> ligands, or just #include .itp files after the fact? If the latter,
>> then you have to modify the coordinate file (conf.gro) to include
>> these molecules. If you did this but did not correctly increment
>> the number of atoms in the second line of the .gro file, likely
>> anything with a higher atom number got truncated. If the conf.gro
>> file you show below is indeed what you used, though, I see no reason
>> why this should have happened except that perhaps you left out a
>> step you thought you had done previously.
>>
>> The difference in the coordinate file vs. topology is 30 atoms,
>> which is more than both of your ligands (20 atoms), so your problem
>> likely lies elsewhere.
>>
>> -Justin
>>
>>
>> Thanks in advance
>>
>> _*conf.gro:*_
>> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>> 5354
>> 2GLN N 1 1.458 -1.158 0.739
>> 2GLN H1 2 1.520 -1.083 0.763
>> ...
>> 485HOH HW1 5333 0.221 -3.864 -2.291
>> 485HOH HW2 5334 0.303 -3.946 -2.407
>> 1EDO OAB 1 0.625 -3.071 -0.171
>> 1EDO HAA 2 0.698 -3.048 -0.107
>> 1EDO CAA 3 0.596 -3.211 -0.163
>> 1EDO CAC 4 0.486 -3.247 -0.261
>> 1EDO OAD 5 0.365 -3.179 -0.224
>> 1EDO HAB 6 0.292 -3.203 -0.288
>> 1TRS O1 1 1.825 -3.900 0.047
>> 1TRS HAA 2 1.853 -3.860 -0.040
>> 1TRS C1 3 1.712 -3.977 0.028
>> 1TRS C 4 1.659 -4.044 0.150
>> 1TRS C3 5 1.576 -3.946 0.226
>> 1TRS O3 6 1.634 -3.824 0.256
>> 1TRS HAC 7 1.569 -3.768 0.307
>> 1TRS N 8 1.582 -4.159 0.113
>> 1TRS HAE 9 1.547 -4.204 0.195
>> 1TRS HAF 10 1.505 -4.131 0.056
>> 1TRS HAD 11 1.639 -4.223 0.062
>> 1TRS C2 12 1.776 -4.085 0.233
>> 1TRS O2 13 1.887 -4.122 0.160
>> 1TRS HAB 14 1.961 -4.148 0.222
>> 8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550
>> 0.00000 0.00000 0.00000
>>
>>
>>
>>
>>
>> -- Ahmet YILDIRIM
>>
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users@gromacs.org
>> <mailto:gmx-users@gromacs.org>
>>
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>>
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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 list gmx-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
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>
--
Ahmet YILDIRIM
--
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