AMBER Archive (2009)

Subject: Re: [AMBER] large resp charges for non-natural amino acid

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Thu Jan 29 2009 - 15:38:12 CST

Hi, Francois,

I see. I would appreciate lot if you could run RED on the server as we
still have no access it (my PI asked out legal office to approve the
usage of RED ... - it takes time). I have two amino acids actually. I
will attach two tar.gz files. If you could run both or one - great!

Best
Arturas

FyD wrote:
> Dear Arturas,
>
>> My system is just a simple peptide that binds into another protein. So,
>> I need just one independent modified amino acid to develop. Initial
>> conformation I have chosen to minimize with Gaussian was manually
>> created to cover essential geometry changes could happen. To be
>> precise, the number of ESP points is much less than in A1 (new)
>> tutorial - I used Gaussian run based on antechamber creates Gaussian
>> input. The number of ESP points is ~8000 and 22 atoms. This
>> alpha-carboxyl-glutamic acid has charge -2. I guess this is the source
>> of all level, but maybe I'm wrong, because I try first time to go for
>> charge derivation for amber FF. I want to stick to standard ff99SB as
>> close as possible in charge scheme. One important point - I have used
>> resp within AMBER 9 distro.
>>
>> After many many different tries playing with resp modifying fitting
>> procedure, I could not get any reasonable charge on CA. It was the only
>> atom which was spoiling all fitting. Also tried to target fitting
>> charges to Mulliken from Gaussian output - helped not much. As far as
>> amber FF tends to use fitted charges, it shoul be used all residue (not
>> like e.g. CHARMM where you can have sero-charge fragments). Something
>> worked than I compared my residue to standard GLU and ASP. Along with
>> caps, I have frozen NH, CO to GLU and ASP values (they are the same).
>> ALSO, I manually put charge -0.05 on CA (something more negative than
>> standard GLU/ASP as my reside is -2 e). After playing with restrains I
>> managed to get "rational" charge scheme. Using this approach my
>> aliphatics hydrogens (CB,...) are positive and carbons negative
>> (physically expected, but in opposite to ff99). Maybe amber community
>> will not crucify for this approach :)
>
> Let's forget all that.
>
>> Gaussian outputs are attached in tar.gz.
>
> I guess these 3 Gaussian outputs correspond to optimized geometries
> because what you sent me are single points. Using the files you sent
> me (considered as geometry optimization outputs), I did a basic test
> using R.E.D.-IV (this can be done with R.E.D.-III.1 as well) and the
> P2N file provided below as a starting point. Here, is what I got using
> four molecular orientations for each optimized conformation:
>
> [fyd_at_master0 R.E.D.IV]$ grep "CA" Mol_MM/*.mol2
> Conf._1:
> Mol_m1-o1-mm2.mol2: 3 CA -0.787076 -0.247015 0.153977 C 1 UNK
> 0.2950
> Conf._2:
> Mol_m2-o1-mm2.mol2: 3 CA -0.761947 -0.217922 0.106399 C 1 UNK
> 0.1043
> Conf._3:
> Mol_m3-o1-mm2.mol2: 3 CA 0.575288 0.129971 0.191250 C 1 UNK
> 0.0932
> Conf._1+2+3:
> Mol_m4-o1-mm2.mol2: 3 CA -0.787076 -0.247015 0.153977 C 1 UNK
> 0.2410
> Mol_m4-o2-mm2.mol2: 3 CA -0.761947 -0.217922 0.106399 C 1 UNK
> 0.2410
> Mol_m4-o3-mm2.mol2: 3 CA 0.575288 0.129971 0.191250 C 1 UNK
> 0.2410
>
> (last column: charge values)
>
> The stricking differences between CA charges (conformations 1, 2 & 3:
> 0.1 up to 0.3!) come from the fact that you have various salt
> briges... I also looked at ESP charges; all is fine for me.
>
> I think you should use R.E.D. & follow what is described @
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
>
> Tell me what you want me to do... Do you want to send me your whole
> job as a single .tar.gz file so that I can look at what goes wrong ?
> (in this case rename all the .com files into .com.o because our mail
> server rejected all .tgz file with .exe/.com files; protection against
> viruses).
>
>> P.S.-1I have checked AMBER mailing list regarding resp - tons of
>> messages. I could not find something direct what is the *standard*
>> procedure to develop charges for amino acids ?
>
> P. Cieplak, W.D. Cornell, C. Bayly & P.A. Kollman, Application of the
> multimolecule and multiconformational RESP methodology to biopolymers:
> Charge derivation for DNA, RNA, and proteins. J. Comput. Chem. 1995,
> 16, 1357-1377
>
> regards, Francois
>
> A typical P2N file to get quick results with R.E.D.-III/IV:
>
> REMARK TITLE beta-carboxylate-glutamic_acid
> REMARK CHARGE-VALUE -2
> REMARK MULTIPLICITY-VALUE 1
> REMARK
> REMARK INTRA-MCC 0.0 | 1 2 3 4 5 6 | Remove
> REMARK INTRA-MCC 0.0 | 21 22 23 24 25 26 | Remove
> REMARK
> REMARK REORIENT 7 9 19 | 19 9 7 | 7 9 11 | 11 9 7
> REMARK
> ATOM 1 H141 UNK 1 3.102 -3.150 0.725 H11
> ATOM 2 C14 UNK 1 2.600 -3.011 -0.229 C1
> ATOM 3 H142 UNK 1 1.697 -3.612 -0.222 H12
> ATOM 4 H143 UNK 1 3.255 -3.331 -1.028 H13
> ATOM 5 C2 UNK 1 2.251 -1.541 -0.423 C2
> ATOM 6 O3 UNK 1 2.817 -0.873 -1.254 O2
> ATOM 7 N4 UNK 1 1.307 -1.103 0.425 N
> ATOM 8 H4 UNK 1 0.674 -1.808 0.771 H
> ATOM 9 C5 UNK 1 0.575 0.130 0.191 CA
> ATOM 10 H5 UNK 1 0.163 0.129 -0.806 HA
> ATOM 11 CT6 UNK 1 -0.600 0.216 1.204 CB
> ATOM 12 H6 UNK 1 -0.329 -0.367 2.076 HB1
> ATOM 13 H6 UNK 1 -0.706 1.245 1.537 HB2
> ATOM 14 C7 UNK 1 -1.954 -0.257 0.652 CG
> ATOM 15 H7 UNK 1 -2.632 -0.333 1.502 HG
> ATOM 16 C8 UNK 1 -1.869 -1.718 0.104 CD1
> ATOM 17 O9 UNK 1 -1.110 -2.474 0.765 OG1
> ATOM 18 O9 UNK 1 -2.548 -2.026 -0.864 OG2
> ATOM 19 C10 UNK 1 1.422 1.386 0.327 C
> ATOM 20 O11 UNK 1 2.414 1.499 1.006 O
> ATOM 21 N12 UNK 1 0.877 2.417 -0.359 N3
> ATOM 22 H12 UNK 1 -0.064 2.270 -0.698 H3
> ATOM 23 C13 UNK 1 1.360 3.754 -0.174 C4
> ATOM 24 H131 UNK 1 2.422 3.809 -0.384 H41
> ATOM 25 H132 UNK 1 0.836 4.411 -0.859 H42
> ATOM 26 H133 UNK 1 1.207 4.124 0.840 H43
> ATOM 27 C8 UNK 1 -2.585 0.818 -0.277 CD2
> ATOM 28 O9 UNK 1 -3.797 0.987 -0.187 OG3
> ATOM 29 O9 UNK 1 -1.790 1.481 -0.988 OG4
> CONECT 1 2
> CONECT 2 1 3 4 5
> CONECT 3 2
> CONECT 4 2
> CONECT 5 1 6 7
> CONECT 6 5
> CONECT 7 5 8 9
> CONECT 8 7
> CONECT 9 7 10 11 19
> CONECT 10 9
> CONECT 11 9 12 13 14
> CONECT 12 11
> CONECT 13 11
> CONECT 14 11 15 16 27
> CONECT 15 14
> CONECT 16 14 17 18
> CONECT 17 16
> CONECT 18 16
> CONECT 19 9 20 21
> CONECT 20 19
> CONECT 21 19 22 23
> CONECT 22 21
> CONECT 23 21 24 25 26
> CONECT 24 23
> CONECT 25 23
> CONECT 26 23
> CONECT 27 14 28 29
> CONECT 28 27
> CONECT 29 27
> END
>
>
>
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> 

-- 

Arturas Ziemys, PhD
  School of Health Information Sciences
  University of Texas Health Science Center at Houston
  7000 Fannin, Suit 880
  Houston, TX 77030
  Phone: (713) 500-3975
  Fax:   (713) 500-3929

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